Maintaining and restoring hydrologic habitat connectivity in mediterranean streams: an integrated modeling framework

Hydrologic alterations designed to provide a stable water supply and to prevent flooding are commonly used in mediterranean-climate river (med-rivers) basins, and these alterations have led to habitat loss and significant declines in aquatic biodiversity. Often the health of freshwater ecosystems depends on maintaining and recovering hydrologic habitat connectivity, which includes structural components related to the physical landscape, functionality of flow dynamics, and an understanding of species habitat requirements for movement, reproduction, and survival. To advance our understanding of hydrologic habitat connectivity and benefits of habitat restoration alternatives we provide: (1) a review of recent perspectives on hydrologic connectivity, including quantitative methods; and (2) a modeling framework to quantify the effects of restoration on hydrologic habitat connectivity. We then illustrate this approach through a case study on lateral hydrologic habitat connectivity that results from channel restoration scenarios using scenarios with different historic and climate-change flows to restore fish floodplain habitat in a med-river, the San Joaquin River, California. Case study results show that in addition to the channel alterations, higher flows are required to recover significant flooded habitat area, especially given reductions in flows expected under climate change. These types of studies will help the planning for restoration of hydrologic habitat connectivity in med-rivers, a critical step for mediterranean species recovery.     

The Significance of Meander Restoration for the Hydrogeomorphology and Recovery of Wetland Organisms in the Kushiro River,a Lowland River in Japan

The meanders and floodplains of the Kushiro River were restored in March 2011. A 1.6‐km stretch of the straightened main channel was remeandered by reconnecting the cutoff former channel and backfilling the straightened reach, and a 2.4‐km meander channel was restored. Additionally, flood levees were removed to promote river–floodplain interactions. There were four objectives of this restoration project: to restore the in‐stream habitat for native fish and invertebrates; to restore floodplain vegetation by increasing flooding frequency and raising the groundwater table; to reduce sediment and nutrient loads in the core wetland areas; to restore a river–floodplain landscape typical to naturally meandering rivers. In this project, not only the natural landscape of a meandering river but also its function was successfully restored. The monitoring results indicated that these goals were likely achieved in the short term after the restoration. The abundance and species richness of fish and invertebrate species increased, most likely because the lentic species that formerly inhabited the cutoff channel remained in the backwater and deep pools created in the restored reach. In addition, lotic species immigrated from neighboring reaches. The removal of flood levees and backfilling of the formerly straightened reach were very effective in increasing the frequency of flooding over the floodplains and raising the water table. The wetland vegetation recovered rapidly 1 year after the completion of the meander restoration. Sediment‐laden floodwater spread over the floodplain, and approximately 80–90% of the fine sediment carried by the water was filtered out by the wetland vegetation.     

Flood regime,dam regulation and fish in the Upper Paraná River: effects on assemblage attributes,reproduction and recruitment

The flood regime is the most important force determining seasonality in neotropical rivers. In the Upper Paran River floodplain, it is the primary factor influencing biological processes. The aim of this paper is to summarize information on the influence of dam-controlled floods on some fish assemblage attributes, reproduction and recruitment in the Upper Paran River floodplain, providing preliminary guidelines for dam operation upstream. Fish were collected in different habitats of the Upper Paran River floodplain (river, channels and lagoons) in the period from 1986 to 2001. The high water period in the Paran River usually occurs from November/December to April/May. Annual variation in the hydrograph affects species with distinct life history strategies differently, and influences the composition and structure of fish assemblages. Large floods were associated with higher species richness. Frequencies of individuals with ripe and partially spent gonads, which indicate spawning, were higher during the period of increasing water level. Dependence on floods seems to be lowest in sedentary species that develop parental care, and highest in large migratory species that spawn in the upper stretches of the basin and use flooded areas as nurseries. Migratory fishes were favored by annual floods that lasted more than 75 days, with longer floods yielding larger populations. The occurrence of high water levels at the beginning of summer is fundamental to the spawning success of migratory species. However, the flood may be less important for recruitment of juveniles if it is of short duration. Dam operation upstream (releasing more water during the raining season) has potential to promote greater floods with appropriate duration improving recruitment, particularly for migratory species.     

Mediterranean-climate streams and rivers: geographically separated but ecologically comparable freshwater systems

Streams and rivers in mediterranean-climate regions (med-rivers in med-regions) are ecologically unique, with flow regimes reflecting precipitation patterns. Although timing of drying and flooding is predictable, seasonal and annual intensity of these events is not. Sequential flooding and drying, coupled with anthropogenic influences make these med-rivers among the most stressed riverine habitat worldwide. Med-rivers are hotspots for biodiversity in all med-regions. Species in med-rivers require different, often opposing adaptive mechanisms to survive drought and flood conditions or recover from them. Thus, metacommunities undergo seasonal differences, reflecting cycles of river fragmentation and connectivity, which also affect ecosystem functioning. River conservation and management is challenging, and trade-offs between environmental and human uses are complex, especially under future climate change scenarios. This overview of a Special Issue on med-rivers synthesizes information presented in 21 articles covering the five med-regions worldwide: Mediterranean Basin, coastal California, central Chile, Cape region of South Africa, and southwest and southern Australia. Research programs to increase basic knowledge in less-developed med-regions should be prioritized to achieve increased abilities to better manage med-rivers.     

Importance of low-flow and high-flow characteristics to restoration of riparian vegetation along rivers in arid south-western United States

1. Riparian vegetation in dry regions is influenced by low‐flow and high‐flow components of the surface and groundwater flow regimes. The duration of no‐flow periods in the surface stream controls vegetation structure along the low‐flow channel, while depth, magnitude and rate of groundwater decline influence phreatophytic vegetation in the floodplain. Flood flows influence vegetation along channels and floodplains by increasing water availability and by creating ecosystem disturbance. 2. On reference rivers in Arizona's Sonoran Desert region, the combination of perennial stream flows, shallow groundwater in the riparian (stream) aquifer, and frequent flooding results in high plant species diversity and landscape heterogeneity and an abundance of pioneer wetland plant species in the floodplain. Vegetation changes on hydrologically altered river reaches are varied, given the great extent of flow regime changes ranging from stream and aquifer dewatering on reaches affected by stream diversion and groundwater pumping to altered timing, frequency, and magnitude of flood flows on reaches downstream of flow‐regulating dams. 3. As stream flows become more intermittent, diversity and cover of herbaceous species along the low‐flow channel decline. As groundwater deepens, diversity of riparian plant species (particularly perennial species) and landscape patches are reduced and species composition in the floodplain shifts from wetland pioneer trees (Populus, Salix) to more drought‐tolerant shrub species including Tamarix (introduced) and Bebbia. 4. On impounded rivers, changes in flood timing can simplify landscape patch structure and shift species composition from mixed forests composed of Populus and Salix, which have narrow regeneration windows, to the more reproductively opportunistic Tamarix. If flows are not diverted, suppression of flooding can result in increased density of riparian vegetation, leading in some cases to very high abundance of Tamarix patches. Coarsening of sediments in river reaches below dams, associated with sediment retention in reservoirs, contributes to reduced cover and richness of herbaceous vegetation by reducing water and nutrient‐holding capacity of soils. 5. These changes have implications for river restoration. They suggest that patch diversity, riparian plant species diversity, and abundance of flood‐dependent wetland tree species such as Populus and Salix can be increased by restoring fluvial dynamics on flood‐suppressed rivers and by increasing water availability in rivers subject to water diversion or withdrawal. On impounded rivers, restoration of plant species diversity also may hinge on restoration of sediment transport. 6. Determining the causes of vegetation change is critical for determining riparian restoration strategies. Of the many riparian restoration efforts underway in south‐western United States, some focus on re‐establishing hydrogeomorphic processes by restoring appropriate flows of surface water, groundwater and sediment, while many others focus on manipulating vegetation structure by planting trees (e.g. Populus) or removing trees (e.g. Tamarix). The latter approaches, in and of themselves, may not yield desired restoration outcomes if the tree species are indicators, rather than prime causes, of underlying changes in the physical environment.     

The influence of floods and precipitation on <Emphasis Type="Italic">Tamarix</Emphasis> establishment in Grand Canyon,Arizona: consequences for flow regime restoration

Decoupling of climate and hydrology combined with introduction of non-native species creates novel abiotic and biotic conditions along highly regulated rivers. Tamarix, a non-native shrub, dominates riparian assemblages along many waterways in the American Southwest, including the Colorado River through Grand Canyon. We conducted a tree-ring study to determine the relative influences of climate and hydrology on Tamarix establishment in Grand Canyon. Riparian vegetation was sparse and annually scoured by large floods until completion of Glen Canyon Dam, which allowed pioneer species, including Tamarix, to expand. Post-dam floods in the mid-1980s were associated with high Tamarix mortality but also initiated a large establishment event. Subsequent establishment has been low but continuous with some exceptions. From 1984 to 2006 establishment increased during years of high, late-summer flows followed by years of low precipitation. This combination provided moist surfaces for Tamarix establishment and may have caused reduced erosion of seedlings or reduced competition from native plants. Attempts to mimic pre-dam floods for ecosystem restoration through planned flood releases also have affected Tamarix establishment. Early (March 1996) and late (November 2004) restoration floods limited establishment, but a small restoration flood in May 2000 followed by steady summer flows permitted widespread establishment. Flood restoration is not expected to prevent Tamarix spread in this system because historic flood timing in May–July coincides with seed release. To decrease future Tamarix establishment, river managers should avoid floods during peak Tamarix seed release, which encompasses the historic spring and early summer flooding period. Tamarix dominance may be reduced by early spring floods that initiate asexual reproduction of clonal shrubs (e.g., Salix exigua, Pluchea sericea).     

River restoration for macroinvertebrate communities in lowland rivers: insights from restorations of the Shibetsu River,north Japan

Because of human impacts, lowland rivers are among the most degraded running water ecosystems, with their floodplains being the center of human activity. Recently, many programs to restore running water ecosystems have been undertaken using various methods in streams and rivers of North America, Europe, and Far East Asia. However, research and knowledge on the effects of river restoration in lowland rivers are limited around the world. The restoration project involving the first reconstruction of a meandering channel in Asia has been conducted in a lowland river section of the Shibetsu River, northern Japan. We review the geomorphologic and hydraulic characteristics of lowland rivers and their environments for macroinvertebrates and discuss approaches to restoring macroinvertebrate communities in lowland rivers, using insights from the restoration project in the Shibetsu River. It is concluded that the recovery of macroinvertebrate assemblages in channelized lowland rivers requires the implementation of restoration methods to create stable substrates.     

The effects of land use changes on streams and rivers in mediterranean climates

We reviewed the literature on the effects of land use changes on mediterranean river ecosystems (med-rivers) to provide a foundation and directions for future research on catchment management during times of rapid human population growth and climate change. Seasonal human demand for water in mediterranean climate regions (med-regions) is high, leading to intense competition for water with riverine communities often containing many endemic species. The responses of river communities to human alterations of land use, vegetation, hydrological, and hydrochemical conditions are similar in mediterranean and other climatic regions. High variation in hydrological regimes in med-regions, however, tends to exacerbate the magnitude of these responses. For example, land use changes promote longer dry season flows, concentrating contaminants, allowing the accumulation of detritus, algae, and plants, and fostering higher temperatures and lower dissolved oxygen levels, all of which may extirpate sensitive native species. Exotic species often thrive in med-rivers altered by human activity, further homogenizing river communities worldwide. We recommend that future research rigorously evaluate the effects of management and restoration practices on river ecosystems, delineate the cause–effect pathways leading from human perturbations to stream biological communities, and incorporate analyses of the effects of scale, land use heterogeneity, and high temporal hydrological variability on stream communities.     

Aquatic plant diversity in riverine wetlands: the role of connectivity

1. The hypothesis was tested that intermediate connectivity to a river results in propagule inputs to wetlands, whereas excessive connectivity impedes recruitment, and insufficient connectivity causes less competitive species to be eliminated, with no recruitment of new species. As a consequence, very low or very high nutrient levels should decrease species richness by selecting specialized species, whereas intermediate nutrient levels should favour the co-occurrence of species with contrasting nutrient requirements. 2. Among cut-off channels with high sinuosity and which are infrequently flooded by the river (low flood scouring), one example possesses high species richness because most species are saved from extinction by long-term isolation of the channel and cold groundwater supplies. Other channels are poorly supplied with groundwater and show a lower richness of species, because of low propagule inputs and low recruitment potential. 3. Cut-off channels with low sinuosity and which are flooded at intermediate frequencies were divided into three groups. The first group was species-poor, being closely connected to the river through downstream backflows which maintain nutrient-rich and turbid waters, in keeping with the hypothesis. The second group presents intermediate richness caused by: (i) lower river backflows; and (ii) floods that partly scour substrate and plants, and afford regeneration niches for transported propagules. The third group was species-poor because of excessive groundwater supplies, which probably acted as a limiting factor for species growth and recruitment. 4. The most frequently flooded channel shows the highest species richness, and occurrence of rare and fugitive species, because of floods which compensate competition by scouring sediments and plants, and afford regeneration niches for propagules. In this case, conservation of biodiversity necessitates propagule sources at the level of the river landscape.     

Riparian Forest Restoration Along Large Rivers: Initial Results from the Sacramento River Project

Restoration of riparian vegetation along large rivers is complicated by the patchiness of the habitat and by conflicts with the societal need to control flooding. The Sacramento River Project, led by The Nature Conservancy in northern California, is testing whether it is possible to restore native forest along a large river without removing flood control. We conducted a post-hoc analysis of monitoring data collected by the project on 1–4-year old plantings of 10 native trees and shrubs at five sites. Two questions of general interest were: Can one identify types of species or sites that are especially suitable for restoration in such riparian habitats? To what degree must sites be treated as mosaics of patches, with different types of patches that are suited to different species? Plant performance as measured by height was better in species of Salicaceae or in species planted as cuttings than in species of other families or in species planted as seedings or seeds. Three within-site factors, land form, soil depth to a buried layer of sand or gravel, and soil texture, affected the growth of several species, indicating that sites do need to be treated as patchy. However, there was little evidence that different species performed better on different types of patches. Instead, areas with deep or fine soils seemed to be favorable for a number of species. Results suggest that it is feasible to re-establish native trees and shrubs along large, regulated rivers, at least at certain sites for an initial period of several years with the aid of weed control and irrigation. Shallowly buried layers or lenses of gravel or sand are a hidden, fine-scale factor that can reduce plant growth on river terraces.     

Impact of hydrology on the chemistry and phytoplankton development in floodplain lakes along the Lower Rhine and Meuse

The impact of hydrology (floods, seepage) on the chemistry of water and sediment in floodplain lakes was studied by a multivariate analysis (PCA) of physico-chemical parameters in 100 lakes within the floodplains in the lower reaches of the rivers Rhine and Meuse. In addition, seasonal fluctuations in water chemistry and chlorophyll-a development in the main channel of the Lower Rhine and five floodplain lakes along a flooding gradient were monitored. The species composition of the summer phytoplankton in these lakes was studied as well.At present very high levels of chloride, sodium, sulphate, phosphate and nitrate are found in the main channels of the rivers Rhine and Meuse, resulting from industrial, agricultural and domestic sewage. Together with the actual concentrations of major ions and nutrients in the main channel, the annual flood duration determines the physico-chemistry of the floodplain lakes. The river water influences the water chemistry of these lakes not only via inundations, but also via seepage. A comparison of recent and historical chemical data shows an increase over the years in the levels of chloride both in the main channel of the Lower Rhine and in seepage lakes along this river. Levels of alkalinity in floodplain lakes showed an inverse relationship with annual flood duration, because sulphur retention and alkalinization occurred in seepage waters and rarely-flooded lakes. The input of large quantities of nutrients (N, P) from the main channel has resulted, especially in frequently flooded lakes, in an increase in algal biomass and a shift in phytoplankton composition from a diatom dominated community towards a community dominated by chlorophytes and cyanobacteria.     

Can environmental flows moderate riparian invasions? The influence of seedling morphology and density on scour losses in experimental floods

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Fish larvae, growth and biomass relationships in an Australian arid zone river: links between floodplains and waterholes

1. Floodplain inundation provides many benefits to fish assemblages of floodplain river systems, particularly those with a predictable annual flood pulse that drives yearly peaks in fish production. In arid‐zone rivers, hydrological patterns are highly variable and the influence of irregular floods on fish production and floodplain energy subsidies may be less clear‐cut. To investigate the importance of floodplain inundation to a dryland river fish assemblage, we sampled fish life stages on the floodplain of Cooper Creek, an Australian arid‐zone river. Sampling was focused around Windorah during a major flood in January 2004 and in isolated waterholes in March 2004 following flood drawdown. 2. Of the 12 native species known to occur in this region, 11 were present on the floodplain, and all were represented by at least two of three life‐stages – larvae, juveniles or adult fish. Late stage larvae of six fish species were found on the floodplain. There were site‐specific differences in larval species assemblages, individual species abundances and larval distribution patterns among floodplain sites. 3. Significant growth was evident on the floodplain, particularly by larval and juvenile fish, reflecting the combination of high water temperatures and shallow, food rich habitats provided by the relatively flat floodplain. 4. Low variation in biomass, species richness and presence/absence of juvenile and adult fish across four floodplain sites indicates consistently high fish productivity across an extensive area. 5. Similarities and differences in fish biomass between the floodplain and isolated post‐flood waterholes suggest high rates of biomass transfer (involving the most abundant species) into local waterholes and, potentially, biomass transfer by some species to other waterholes in the catchment during floodplain inundation and after floods recede. 6. The high concentration of fish on this shallow floodplain suggests it could be a key area of high fish production that drives a significant proportion of waterhole productivity in the vicinity. The Windorah floodplain provides favourable conditions necessary for the spawning of some species and juvenile recruitment of the majority of species. It is also appears to be a significant conduit for the movements of fish that underpin high genetic similarity, hence population mixing, of many species throughout the Cooper Creek catchment. The high floodplain fish production in turn provides a significant energy subsidy to waterholes after floodwaters recede. 7. The identification of key sites of high fish production, such as the Windorah floodplain, may be important from a conservation perspective. Key management principles should be: maintenance of the natural flooding regime; identification of the most productive floodplain areas; and maintenance of their connectivity to anastomosing river channels and the remnant aquatic habitats that ultimately sustain this fish assemblage through long‐term dry/drought and flood cycles.     

Anomalous droughts,not invasion,decrease persistence of native fishes in a desert river

Changing climate extremes and invasion by non‐native species are two of the most prominent threats to native faunas. Predicting the relationships between global change and native faunas requires a quantitative toolkit that effectively links the timing and magnitude of extreme events to variation in species abundances. Here, we examine how discharge anomalies – unexpected floods and droughts – determine covariation in abundance of native and non‐native fish species in a highly variable desert river in Arizona. We quantified stochastic variation in discharge using Fourier analyses on >15 000 daily observations. We subsequently coupled maximum annual spectral anomalies with a 15‐year time series of fish abundances (1994–2008), using Multivariate Autoregressive State‐Space (MARSS) models. Abiotic drivers (discharge anomalies) were paramount in determining long‐term fish abundances, whereas biotic drivers (species interactions) played only a secondary role. As predicted, anomalous droughts reduced the abundances of native species, while floods increased them. However, in contrast to previous studies, we observed that the non‐native assemblage was surprisingly unresponsive to extreme events. Biological trait analyses showed that functional uniqueness was higher in native than in non‐native fishes. We also found that discharge anomalies influenced diversity patterns at the meta‐community level, with nestedness increasing after anomalous droughts due to the differential impairment of native species. Overall, our results advance the notion that discharge variation is key in determining community trajectories in the long term, predicting the persistence of native fauna even in the face of invasion. We suggest this variation, rather than biotic interactions, may commonly underlie covariation between native and non‐native faunas, especially in highly variable environments. If droughts become increasingly severe due to climate change, and floods increasingly muted due to regulation, fish assemblages in desert rivers may become taxonomically and functionally impoverished and dominated by non‐native taxa.     

Impacts of hydrological restoration on lowland river floodplain plant communities

Many lowland floodplain habitats have been disconnected from their rivers by flood defence banks. Removing or lowering these banks can reinstate regular flooding and thus restore these important wetland plant communities. In this study we analyse changes in wetland hydrology and plant community composition following the lowering of flood defence banks at a floodplain of the River Don in the United Kingdom (UK). The aim of the restoration project was to improve the quality of “floodplain grazing marsh” habitat, which is a group of wetland communities that are of conservation interest in the UK. We analyse changes in species richness and community composition over a period of 6 years, and compare the presence of indicator species from the target floodplain grazing marsh plant communities. The lowering of the flood banks increased the frequency of flood events, from an estimated average of 1.7 floods per year to 571 floods per year. The increased flooding significantly increased the proportion of time that the wetland was submerged, and the heterogeneity in hydrological conditions within the floodplain. There were significant differences in composition between the pre-restoration and restored plant communities. Plants with traits for moisture tolerance became more abundant, although the communities did not contain significantly more ‘target’ floodplain grazing marsh species at the end of the study period than prior to restoration. Colonisation by floodplain grazing marsh species may have been limited because environmental conditions were not yet suitable, or because of a shortage of colonising propagules. While the desired target plant community has not been achieved after 5 years, it is encouraging that the community has changed dynamically as a result of hydrological changes, and that moisture-tolerant species have increased in occurrence. Over the next few decades, the restored flood regime may cause further environmental change or colonisation events, thus helping increase the occurrence of desired floodplain grazing marsh indicator species.

     

Aquatic plant diversity in four river floodplains: a comparison at two hierarchical levels

The present study focuses on the role ofenvironmental factors in plant diversity and community organization at both water-body and river floodplain levels. The cover of each plant species was measured at 841 sampling plots along 63 cut-off channels located in four river floodplains. Environmental variables were documented either at river level (suspended matter, water physico-chemistry, river slope) or at cut-off channel level (channel capacity, slope, substrate grain-size). At both river and cut-off channel levels, increasing slope (i.e. increasing erosion during floods) and decreasing nutrient-content of the water raise species richness and uniqueness (number of species found only in one river), according to hypotheses on the combined role of disturbances and productivity in biodiversity. Rivers that are not eroded during floods are nutrient-rich and present the lowest richness and uniqueness at the river level, but dewatering combined with high connectivity increase richness at the cut-off channel level.     

Comparing the fish assemblages and food‐web structures of large floodplain rivers

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Post-Flood Recovery of a Macroinvertebrate Community in a Regulated River: Resilience of an Anthropogenically Altered Ecosystem

Preservation of biodiversity depends on restoring the full range of historic environmental variation to which organisms have evolved, including natural disturbances. Lotic ecosystems have been fragmented by dams causing a reduction in natural levels of environmental variation (flow and temperature) and consequently a reduction of biodiversity in downstream communities. We conducted a long‐term study of the macroinvertebrate communities before and after natural flood disturbances in an unregulated reference site (natural flows and temperatures), a regulated site (regulated flows and temperatures), and a partially regulated reference site (regulated flows and natural temperatures) on the upper Colorado River downstream from a deep‐release storage reservoir. We aimed to test the hypothesis that floods and temperature restoration would cause an increase in macroinvertebrate diversity at the regulated site. Over the short term, macroinvertebrate richness decreased at the regulated site when compared to pre‐flood levels, whereas total macroinvertebrate density remained unchanged. Over the long term (1 and 10 years after the floods), macroinvertebrate diversity and community structure at the regulated site returned to pre‐flood levels without increasing to reference conditions. Occasional floods did not restore biodiversity in this system. As long as the physical state variables remain altered beyond a threshold, the community will return to its altered regulated condition. However, temperature restoration at the partially regulated site resulted in an increase in macroinvertebrate diversity. Our results indicate that restoration of the natural temperature regime will have a stronger effect on restoring biodiversity than occasional channel‐forming floods.     

Success of Instream Habitat Structures After a 50-Year Flood in Gold Creek, Montana

Gold Creek, in western Montana, lost complexity and diversity of fish habitat following riparian logging activities, removal of instream wood, and subsequent scouring. In the 4.8-km study area, the stream was almost totally void of large woody debris (4.2 pieces/km) and associated pools (1.3 pools/km). We constructed 66 structures made of natural materials (rock and wood) that resulted in 61 new pools in the study area in an attempt to restore salmonid habitat in the fall of 1996. An estimated 50-year recurrence interval flood occurred in the following spring. Of the original 66 structures, 55 (85%) remained intact and stable. Laterally confined reaches retained significantly more pools than laterally extended reaches. Owing to a history of anthropogenic impacts in forested streams in the intermountain west, restoration efforts are needed. If instream structures are tailored to specific morphologic channel types, fish habitat restoration can be successful and withstand major floods.     

Hydrologic versus geomorphic limitation on CPOM storage in stream ecosystems

1. Stream ecosystems are the products of interactions between hydrology, geomorphology and ecology, but examining all three components simultaneously is difficult and rarely attempted. Frequently, either geomorphology or hydrology is treated as invariable or static. 2. To examine the validity of treating either hydrology or geomorphology as static, we studied the individual and combined effects of hydrology and channel geomorphology on coarse particulate organic matter (CPOM) storage. Using data from an experimental leaf release in a hydrologically regulated stream we created a simple numerical model. This allowed us to quantify the relative influence of CPOM trapping and CPOM retention on total long‐term CPOM storage under variable regimes of flood frequency and geomorphic structure. 3. CPOM storage is a function of supply, flood frequency and the type and frequency of in‐stream structures. In‐stream structures perform two distinct functions, trapping and retention, whose relative importance in leaf storage changes with stream hydrology. Trapping is more important for CPOM storage in streams with few floods, while retention is more important in streams with frequent floods. Different structures (e.g. boulders, large wood, small wood) perform these functions at different efficiencies. We found that large wood trapped two to three times more leaves than the bank, but that the bank retained leaves two to three times more efficiently. 4. A modelled channel with five times the amount of large wood as the study channel (a ‘wood restoration’) initially stored 14% more leaves than the modelled ‘natural’ channel. After six floods, however, the modelled wood restoration channel stored 50% less CPOM than the natural channel as the large wood had high trapping but poor retention. The modelled natural channel contained structures that could both trap and retain. Thus, as different structures performed different functions, the structural complexity buffered the stream allochthonous energy base against changes in hydrology through its balance of trapping and retention. 5. As the frequency of floods increased, the spatial distribution of CPOM became increasingly patchy as storage was driven entirely by structures with high retention. Thus, the coupling of flood frequency and geomorphic structure influenced CPOM availability, which in turn has ramifications for the entire stream food web.