Sediments in Marsh Ponds of the Gulf Coast Chenier Plain: Effects of Structural Marsh Management and Salinity

Physical characteristics of sediments in coastal marsh ponds (flooded zones of marsh associated with little vegetation) have important ecological consequences because they determine compositions of benthic invertebrate communities, which in turn influence compositions of waterbird communities. Sediments in marsh ponds of the Gulf Coast Chenier Plain potentially are affected by (1) structural marsh management (levees, water control structures and impoundments; SMM), and (2) variation in salinity. Based on available literature concerning effects of SMM on sediments in emergent plant zones (zones of marsh occasionally flooded and associated with dense vegetation) of coastal marshes, we predicted that SMM would increase sediment carbon content and sediment hardness, and decrease oxygen penetration (O₂ depth) and the silt-clay fraction in marsh pond sediments. Assuming that freshwater marshes are more productive than are saline marshes, we also predicted that sediments of impounded freshwater marsh ponds would contain more carbon than those of impounded oligohaline and mesohaline marsh ponds, whereas C:N ratio, sediment hardness, silt-clay fraction, and O₂ depth would be similar among pond types. Accordingly, we measured sediment variables within ponds of impounded and unimpounded marshes on Rockefeller State Wildlife Refuge, near Grand Chenier, Louisiana. To test the above predictions, we compared sediment variables (1) between ponds of impounded (IM) and unimpounded mesohaline marshes (UM), and (2) among ponds of impounded freshwater (IF), oligohaline (IO), and mesohaline (IM) marshes. An a priori multivariate analysis of variance (MANOVA) contrast indicated that sediments differed between IM and UM marsh ponds. As predicted, the silt-clay fraction and O₂ depth were lower and carbon content, C:N ratio, and sediment hardness were higher in IM than in UM marsh ponds. An a priori MANOVA contrast also indicated that sediments differed among IF, IO, and IM marsh ponds. As predicted, carbon content was higher in IF marsh ponds than in ponds of other impounded marsh types. In contrast to our predictions, C:N ratio and sediment hardness were lowest and silt-clay fraction and O₂ depth were highest in IO and IM marsh ponds. Our results indicated that SMM has affected physical properties of sediments in coastal marsh ponds. Moreover, sediments in IF marsh ponds were affected more so than were those in IO and IM marsh ponds. Our results, in conjunction with those of previous studies, indicated that sediments of marsh ponds and emergent plant zones differed greatly. We predict that changes in pond sediments due to SMM will promote greater epifaunal macroinvertebrate biomass, which in turn should attract larger populations of wintering waterbirds. However, waterbirds that filter or probe soft sediments may be negatively affected by SMM because of the expected decrease in infaunal invertebrate biomass.     

Spatial and temporal distribution patterns of the macrozoobenthos assemblage in the salt marshes of Tejo estuary (Portugal)

The present study focuses on the spatial and temporal distribution of the macroinvertebrate community of the salt marsh areas of the Tejo estuary, based on surveys conducted from autumn 1998 to summer 2000. Samples were collected quarterly in five different intertidal areas along an elevation gradient in: mudflats, creek mouths, creeks, pioneer salt marsh areas and middle marsh areas. A total of 36 benthic invertebrate taxa were identified. Insect larvae were the most well represented group, with 10 taxa identified. Oligochaetes and ostracods were the most numerically abundant taxa, whereas bivalves dominated in biomass. Benthic macroinvertebrate assemblages were dominated, both in number and biomass, by deposit feeders. Three distinct macroinvertebrate assemblages were distinguished along the elevation gradient, based on species presence, density and biomass: the unvegetated muddy areas with a macrobenthic assemblage composed mostly by infauna; the salt marsh pioneer areas of Spartina maritima in which several epibenthic taxa were found, as well as endobenthic taxa characteristic of muddy sediment; and the creek margins, with epifauna taxa such as insect larvae and crustaceans and a low abundance of benthic infauna. Total biomass in the unvegetated and Spartina areas was higher during spring and summer mainly due to the increase in biomass of Scrobicularia plana and Hydrobia ulvae. No decreases in the salt marsh macroinvertebrate biomass values were observed during the highest densities of their potential nektonic predators (summer). This fact might indicate that macroinvertebrates are not a limiting resource for the nektonic species, and that the natural biomass increment of these invertebrate species could be masking the predation/disturbance caused by the nektonic species.     

Comparison of benthic macroinvertebrate communities by two methods: Kick- and U-net sampling

The assessment of benthic invertebrate community condition is an integral component of freshwater biomonitoring and water quality determination. Several sampling devices have been developed to collect benthic macroinvertebrates, including qualitative, semi-quantitative, and quantitative methods. In this study, we compared several benthic macroinvertebrate metrics and community assemblage measures calculated from data obtained from two sampling methods, namely the Kick- and U-net sampling devices. We reasoned that if the two methods produced similar values for benthic metrics and community composition, then samples collected by these methods should be able to be combined to build larger data sets for use in regional bioassessment analyses. No statistical differences between Kick- and U-net methods were found among standard benthic macroinvertebrate metrics, except for Kick-nets collecting more Chironomidae. Invertebrate assemblages were very similar between collection methods, although slightly greater taxonomic richness was found in U-net samples. Bray–Curtis similarity was typically >75% between methods within a stream, while classification strength-sampling-method comparability, an approach for analyzing differences in similarity between groups, indicated invertebrate assemblage similarity between collection methods was virtually identical at approximately 100%. Since these two methods produce similar results, we conclude that benthic macroinvertebrate data collected by these methods can be combined for data analysis and bioassessments with the caveat that mesh size of the sample nets is similar. In addition, if the primary study objective is to assess macroinvertebrate biodiversity, then the U-net sampling device may be more appropriate, despite the slightly greater time needed to complete field sample collection, as it tended to collect a greater diversity of species.     

Filter and deposit: a potential role of freshwater mussels in ecosystem functioning associated with enhanced macroinvertebrate assemblage structure in a Neotropical river

Hydrobiologia - Mussels provide important ecological functions in freshwater ecosystems but the associations between Amazonian mussels, macroinvertebrate assemblage and habitat quality remain...     

Solar ultraviolet radiation and CO<Subscript>2</Subscript>-induced ocean acidification interacts to influence the photosynthetic performance of the red tide alga <Emphasis Type="Italic">Phaeocystis globosa</Emphasis> (Prymnesiophyceae)

Cattle grazing in riparian areas can reduce water quality, alter stream channel characteristics, and alter fish and macroinvertebrate assemblage structure. The U.S. Department of Agriculture, Natural Resources Conservation Services has recommended Rotational Grazing (RG) as an alternative management method on livestock and dairy operations to protect riparian areas and water quality. We evaluated 13 stream channel characteristics, benthic macroinvertebrate larvae (BML), and chironomid pupal exuviae (CPE) from 18 sites in the Upper Midwest of the United States in relation to RG and conventional grazing (CG). A Biotic Composite Score comprised of several macroinvertebrate metrics was developed for both the BML assemblage and the CPE assemblage. Multi-Response Permutation Procedures (MRPP) indicated a significant difference in stream channel characteristics between RG and CG. Nonmetric Multidimensional Scaling indicated that RG sites were associated with more stable stream banks, higher quality aquatic habitat, lower soil compaction, and larger particles in the streambed. However, neither MRPP nor Mann–Whitney U tests demonstrated a difference in Biotic Composite Scores for BML or CPE along RG and CG sites. The BML and CPE metrics were significantly correlated, indicating that they were likely responding to similar variables among the study sites. Although stream channel characteristics appeared to respond to grazing management, BML and CPE may have responded to land use throughout the watershed, as well as local land use.     

Restoration of dredged canals in wetlands: a comparison of methods

A comparison of two methods for restoring dredged canals to wetlands was examined at the Jean Lafitte National Historical Park and Preserve’s Barataria Preserve Unit near New Orleans, LA. Both northern and southern canals had the remnant dredged spoil material returned to the canal, but the southern canal had additional sediment pumped in from a nearby lake. The water depth in the southern canal shallowed significantly from 1.2 to 0.4 m following backfilling and sediment addition, while the depth of the northern canal (which received no additional sediment) remained unchanged following backfilling. Neither site had complete soil restoration, but the former spoil areas of the northern canal showed greater restoration than the southern canal. The vegetation on the former spoil areas of the northern canal closely resembled that of the reference marsh, while the former spoil areas of the southern canal had species indicative of spoil banks and other elevated areas. After 3 years wetland vegetation was established on approximately 65% of the former spoil areas at both sites and 20–25% of the open water areas. Sediment addition to the southern canal raised costs by a factor of eight times compared to that of the northern canal. The results of this study document the restoration potential of both methods, but also show that backfilling without supplemental sediment additions can restore abandoned canals at a fraction of the cost of other methods.     

A Statistical Evaluation of Sediment Quality Triad Benthic Community Measurements in PAH-Impacted Sediments at a Manufactured Gas Plant Site along the Hudson River

The sediment quality triad (SQT) assumes that three measurements (sediment chemistry, laboratory bioassay, and benthic macroinvertebrate counts) comprise an independent assessment of impact, which when integrated using a weight-of-evidence approach provides a comprehensive assessment of risk. An SQT assessment was conducted on 41 sediment samples collected adjacent to a manufactured gas plant site on the freshwater reach of the Hudson River in New York State. The assessment shows that the benthic macroinvertebrate data did not correlate with either sediment or pore water polycyclic aromatic hydrocarbon (PAH) concentrations, nor did these data show consistent relationships to the results of laboratory bioassay testing (Hyalella azteca 28-day survival or biomass). The benthic community across the site and reference areas was comprised of few taxa, all of which were pollution-tolerant organisms with tolerance values greater than or equal to five. Only in significantly impacted sediment samples with PAH concentrations in the thousands of milligrams per kilogram, pore water concentrations above 100 toxic units, and visible non-aqueous phase liquid present in the sample did the benthic macroinvertebrate data show a response. In contrast, sediment and pore water PAH measurements and H. azteca toxicity testing provided consistent interpretation of impact. These results illustrate that benthic macroinvertebrate data may contain less information value and be a more challenging line of evidence to interpret in triad studies conducted in certain ecological settings; in this case, a large-order river with a relatively depauperate benthic community dominated by species tolerant of PAHs.     

Invaders are not a random selection of species

We assembled information on 119 species of freshwater macroinvertebrate invaders in North America and Europe, and compared them to all native freshwater species in North America and Europe. We tested whether the invaders were a random or selected group among taxa (phylum or class), water quality requirements, and feeding habit. We found that freshwater macroinvertebrate invaders are not a random selection of species, and are over-represented by molluscs and crustaceans, while taxa richness of native communities are dominated by insects. Over 35% of native species of aquatic invertebrates in North America are only able to live in areas with excellent or very good water quality, and are intolerant of organic pollution. In contrast, all invaders are tolerant of at least moderate amounts of organic pollution. There was a significant difference in the distribution of feeding habits between native species and invaders: collector-filterers (including suspension feeders) were 2.5–3 times more abundant, and predators were 3–4 times less abundant among invaders than among native invertebrates. The ongoing spread of exotic species affects the biodiversity of selected taxa, shifts communities toward greater tolerance of organic pollution and increases the numbers of suspension feeders, thereby enhancing benthic pelagic coupling in waterbodies with high densities of invaders. Because these processes are very similar in Europe and North America, we suggest that the observed patterns may have a common global effect.     

The influences of climatic variation and vegetation on stream biota: lessons from the Big Dry in southeastern Australia

Aquatic biodiversity faces increasing threats from climate change, escalating exploitation of water and land use intensification. Loss of vegetation in catchments (= watersheds) has been identified as a substantial problem for many river basins, and there is an urgent need to better understand how climate change may interact with changes in catchment vegetation to influence the ecological condition of freshwater ecosystems. We used 20 years of biological monitoring data from Victoria, southeastern Australia, to explore the influences of catchment vegetation and climate on stream macroinvertebrate assemblages. Southeastern Australia experienced a severe drought from 1997 to 2009, with reductions of stream flows >50% in some areas. The prolonged drying substantially altered macroinvertebrate assemblages, with reduced prevalence of many flow‐dependent taxa and increased prevalence of taxa that are tolerant of low‐flow conditions and poor water quality. Stream condition, as assessed by several commonly used macroinvertebrate indices, was consistently better in reaches with extensive native tree cover in upstream catchments. Prolonged drought apparently caused similar absolute declines in macroinvertebrate condition indices regardless of vegetation cover, but streams with intact catchment and riparian vegetation started in better condition and remained so throughout the drought. The largest positive effects of catchment tree cover on both water quality and macroinvertebrate assemblages occurred above a threshold of ca. 60% areal tree cover in upstream catchments and in higher rainfall areas. Riparian tree cover also had positive effects on macroinvertebrate assemblages, especially in warmer catchments. Our results suggest that the benefits of extensive tree cover via improved water quality and in‐channel habitat persist during drought and show the potential for vegetation management to reduce negative impacts of climatic extremes for aquatic ecosystems.     

Effect of salinity-altering pulsing events on soil organic carbon loss along an intertidal wetland gradient: a laboratory experiment

Salinity changes resulting from storm surge, tides, precipitation, and stormwater run-off are common in coastal wetlands. Soil microbial communities respond quickly to salinity changes, altering the rate of soil organic carbon (SOC) loss and associated biogeochemical processes. This study quantified the impact of salinity-altering pulses on SOC loss, defined as microbial respiration (CO₂ flux) at high and low tide, CH₄ flux, and dissolved OC (DOC) release, in 3 intertidal wetlands (Jacksonville, FL, USA). Intact soil cores from a freshwater tidal, brackish, and salt marsh were exposed to simulated tides and 3 salinity pulsing events during a 53-day laboratory experiment. Soil and water physio-chemical properties, nutrient release, and microbial indicators were measured. Microbial respiration was the dominate pathway of SOC loss (>97 %). Soil hydraulic conductivity was greater in brackish and salt marshes and was critical to overall soil respiration. High tide CO₂ flux was greatest in the freshwater marsh (58 % of SOC loss) and positively correlated with DOC concentration; low tide CO₂ flux was greatest in brackish and salt marshes (62 and 70 % of SOC loss, respectively) and correlated with NH₄ ⁺ and microbial biomass. The freshwater marsh was sensitive to brackish pulses, causing a 112 % increase in respiration, presumably from accelerated sulfate reduction and N-cycling. SOC loss increased in the salt marsh pulsed with freshwater, suggesting freshwater run-off may reduce a salt marsh’s ability to keep-pace with sea level rise. Increased inundation from storm surges could accelerate SOC loss in freshwater marshes, while decreasing SOC loss in brackish and salt marshes.     

How Much Is Enough? Minimal Responses of Water Quality and Stream Biota to Partial Retrofit Stormwater Management in a Suburban Neighborhood

Decentralized stormwater management approaches (e.g., biofiltration swales, pervious pavement, green roofs, rain gardens) that capture, detain, infiltrate, and filter runoff are now commonly used to minimize the impacts of stormwater runoff from impervious surfaces on aquatic ecosystems. However, there is little research on the effectiveness of retrofit, parcel-scale stormwater management practices for improving downstream aquatic ecosystem health. A reverse auction was used to encourage homeowners to mitigate stormwater on their property within the suburban, 1.8 km² Shepherd Creek catchment in Cincinnati, Ohio (USA). In 2007–2008, 165 rain barrels and 81 rain gardens were installed on 30% of the properties in four experimental (treatment) subcatchments, and two additional subcatchments were maintained as controls. At the base of the subcatchments, we sampled monthly baseflow water quality, and seasonal (5×/year) physical habitat, periphyton assemblages, and macroinvertebrate assemblages in the streams for the three years before and after treatment implementation. Given the minor reductions in directly connected impervious area from the rain barrel installations (11.6% to 10.4% in the most impaired subcatchment) and high total impervious levels (13.1% to 19.9% in experimental subcatchments), we expected minor or no responses of water quality and biota to stormwater management. There were trends of increased conductivity, iron, and sulfate for control sites, but no such contemporaneous trends for experimental sites. The minor effects of treatment on streamflow volume and water quality did not translate into changes in biotic health, and the few periphyton and macroinvertebrate responses could be explained by factors not associated with the treatment (e.g., vegetation clearing, drought conditions). Improvement of overall stream health is unlikely without additional treatment of major impervious surfaces (including roads, apartment buildings, and parking lots). Further research is needed to define the minimum effect threshold and restoration trajectories for retrofitting catchments to improve the health of stream ecosystems.     

Land‐use legacy and the differential response of stream macroinvertebrates to multiple stressors studied using in situ experimental mesocosms

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Energetic implications of floodplain wetland restoration strategies for waterfowl

Modifications of the Illinois River and associated tributaries have resulted in altered hydrologic cycles and persistent river‐floodplain connections during the growing season that frequently impede the establishment of hydrophytic vegetation and have reduced value for migratory waterfowl and other waterbirds. To help guide floodplain restoration, we compared energetic carrying capacity for waterfowl in two wetland complexes along the Illinois River under different management regimes during 2012–2015. The south pool of Chautauqua National Wildlife Refuge (CNWR) was seasonally flooded due to a partial river connection and managed for moist‐soil vegetation. Emiquon Preserve was hydrologically isolated from the Illinois River by a high‐elevation levee and managed as a semipermanently flooded emergent marsh. Semipermanent emergent marsh management at Emiquon Preserve produced 5,495 energetic use‐days (EUD)/ha for waterfowl and other waterbirds across wetland cover types and years, and seasonal moist‐soil management at CNWR produced 6,199 EUD/ha in one of 4 years. At Emiquon Preserve, the aquatic bed cover type produced 9,660 EUD/ha, followed by 5,261 EUD/ha in moist‐soil, 1,398 EUD/ha in persistent emergent, 1,185 EUD/ha in hemi‐marsh, and 12 EUD/ha in open water cover types. At CNWR, the annual grass and sedge cover type produced 7,031 EUD/ha, followed by 5,618 EUD/ha in annual broadleaf and 1,305 EUD/ha in perennial grass cover types. Restoration of floodplain wetlands in isolation from frequent flood pulses during the growing season can produce hemi‐marsh and aquatic bed vegetation communities that provide high‐quality habitat for waterfowl and which have been mostly eliminated from large river systems in the Midwest, U.S.A.     

The Effects of Phragmites Removal on Nutrient Pools in a Freshwater Tidal Marsh Ecosystem

Selected nitrogen and phosphorus pools in two freshwater tidal marsh ecosystems on the lower Connecticut River were measured relative to Phragmites, Typha and mixed native wetland plant cover types. For both the Chapman Pond Preserve and Chester Creek Marsh, significant differences were found between plant cover types in porewater ammonium and phosphate for some months during the 1998 growing season; porewater nitrate was always below the detection limit. At Chapman Pond, no significant differences were detected between Phragmites and Typha for plant tissue N concentrations. The standing stock of nitrogen was higher in Phragmites stands, however, owing to its greater aboveground biomass. No significant difference was found between plant cover types for total soil N at Chapman Pond, but KCl extractable ammonium was higher in the mixed cover type than Phragmites or Typha. The results of this study suggest that Phragmites is affecting nutrient pools in freshwater tidal marshes, a result that should be considered in future management design.     

Macroinvertebrate assemblages in Pennsylvania (U.S.A.) springs

Five distinct macroinvertebrate assemblages were identified using cluster analysis of the rank-order abundances of 13 orders in 15 freshwater springs of central Pennsylvania, U.S.A. A principal components analysis of 20 environmental factors indicated that an insect-dominated assemblage occurred in low pH, softwater sandstone springs and an amphipod-dominated assemblage was associated with medium to hardwater springs with a silt to gravel substratum. Three other assemblages were found in hardwater limestone springs: the peracaridan-hydrobiid assemblage was characterized by dense macrophyte beds and a silt to cobble substratum, the peracaridan-triclad-glossosomatid assemblage by a rubbly, gravel-cobble substratum and relatively high discharge, and the peracaridan-hydrobiid-oligochaete assemblage by a silty substratum and dense mats of green algae.Most of the common macroinvertebrate species were associated with specific physical, chemical, and (or) vegetational factors, but abundance associations between species pairs were generally lacking. We infer that assemblages are primarily determined by the match between the environmental mosaic of individual springs and the ecological requirements of the available species, rather than by strong interspecific interactions.Species-environment associations were assessed in an additional study of five closely neighboring springs in which some environmental variables of the wider study were nearly constant.     

Prairie Wolf Slough Wetlands Demonstration Project: A Case Study Illustrating the Need for Incorporating Soil and Water Quality Assessment in Wetland Restoration Planning,Design and Monitoring

In northeastern Illinois, restored wetlands are used to improve water quality in streams degraded by agriculture and urban development. Using freshwater wetlands to reduce nitrogen loading to lakes and rivers is well documented; however, there are fewer studies addressing their use to remove phosphorous. In 1998, a systematic water quality monitoring project was begun at Prairie Wolf Slough Wetland Demonstration Project, a restored palustrine emergent marsh wetland located on an abandoned farm field north of Chicago. The wetland drains 98 ha of mixed land uses into the Chicago River. Our objectives were to assess spatial and temporal variations in total suspended solids, soluble reactive and total phosphorous concentrations, and mass loadings and compute a mass balance and retention efficiency for these constituents. Water sampling was conducted from 1998 to 2003. In 2004, soil samples were collected from the marsh and an adjacent abandoned farm site and analyzed for soil test (Bray) phosphorus. The marsh effectively traps suspended solids but acts as a source of soluble reactive and total phosphorous to the river both during the growing and nongrowing seasons. Net export of phosphorous from the wetland was likely due to mobilization of orthophosphate as a result of anoxic conditions produced during inundation events. Often little consideration is given to the link between soil and water quality when locating restoration sites. Our study adds to a growing body of literature that clearly demonstrates the need for both soil and water quality assessments in wetland restoration planning, design, and monitoring.     

Greater macroinvertebrate diversity and freshwater mussel density in meander margins of an Amazon river

Meanders are complex aquatic environments exhibiting different flow and sediment characteristics that influence macroinvertebrate distribution. Differences in macroinvertebrate composition, freshwater mussel density (mainly Castalia ambigua Lamarck, 1819) and habitat variables were investigated, using uni‐ and multivariate analyses, in two zones, the margin and thalweg, of the meanders of a 7‐km stretch of a morphologically unaltered tropical alluvial lowland river. Clear differences were found between meander zones, with greater taxonomic and functional diversity of macroinvertebrates and greater freshwater mussel densities in the meander margin. A total of 12 families of macroinvertebrates were exclusive to the meander margin, and macroinvertebrate indicators of zones were Philopotamidae and Leptoceridae (meander margin) and Chironomidae and Elmidae (meander thalweg). In the meander margin, there were no differences in macroinvertebrate abundance, and taxonomic and functional group diversity among areas with low, medium and high mussel density. Macroinvertebrate abundance did not vary between zones, but in both, abundance was associated with lower pH and higher electrical conductivity. Low shear velocity, which stabilises the river bed, high organic matter content and percentage silt in the meander margin were associated with higher taxonomic and functional macroinvertebrate diversity, as well as the presence of freshwater mussels. Natural unaltered meanders are spatially heterogeneous in both habitat and biodiversity and, similar to restored meanders, support greater macroinvertebrate taxonomic and functional diversity, as well as maintain freshwater mussel beds, mainly by stabilising the river bed. The meander margin may also be important for attracting mussel host fish that feed on macroinvertebrates and aid mussel dispersal. Thus, the meander margins, and other similar riparian habitats with low shear velocity, for example, side channels and pools, have potentially high conservation value and should be afforded due protection.     

The tidal freshwater reach of the Weser estuary: Riverine or estuarine?

The tidal freshwater reaches of estuaries have received little attention in ecological research although they are often heavily stressed by environmental impacts. We have thus compiled published and previously unpublished data from the Weser Estuary, Germany. Physical, chemical and biological properties are described within the tidal freshwater reach and compared with the upstream (riverine) and downstream (mixohaline) habitats. The tidal freshwater region is different from riverine sites, mainly due to tidally induced physical processes such as prolonged residence time of the water, oscillating water levels and changing current velocities and directions. Distinctions from the mixohaline situation are mainly due to differences in salinity and particulate suspended matter concentration. It is thus possible to define the tidal freshwater reach of the Weser Estuary as a separate biotope with a specific community structure. The phyto- and zooplankton is a mixture of riverine and autochthonous species whereas marine species are almost completely lacking. In the macroinvertebrate component, as well as in the fish community, marine and riverine species are combined with autochthonous species. This is probably typical for the tidal freshwater reaches of many river dominated coastal plain estuaries. We conclude that the tidal freshwater reaches are an important site of physical, chemical and biological processes which may alter riverine input considerably before it reaches the freshwater-seawater interface. For a better understanding of the ecological functioning of estuaries, it is essential to include these areas within estuarine research programmes.     

The influence of reduced flow during a drought on patterns of variation in macroinvertebrate assemblages across a spatial hierarchy in two lowland rivers

1. With the aim of determining whether patterns of variation in macroinvertebrate assemblage composition across the hierarchy of spatial units in two lowland rivers changed during a supra‐seasonal drought (1997–2000), patterns during a reduced flow season (1999–2000) were compared with those during two preceding higher flow seasons (1997–98 and 1998–99) using samples from the Glenelg and Wimmera Rivers, two lowland regulated rivers in western Victoria, Australia. 2. We hypothesised that (i) differences between reaches would increase during the reduced flow season owing to decreased hydrological connectivity, (ii) differences between the habitats would decrease because the cessation of flow in run habitats should cause them to become more similar to pool habitats and (iii) differences between microhabitats would also decrease because of reduced scour of inorganic substrata and large woody debris. 3. During each season, macroinvertebrates were sampled from three microhabitats (sand/silt substratum, large woody debris and macrophytes) that were hierarchically nested within a run or pool habitat and within one of three reaches within each river. A range of physico‐chemical variables was also sampled. 4. Analysis of similarity showed that assemblage composition in both rivers during the higher flow seasons differed more among microhabitats than other spatial units. However, during the reduced flow season, assemblage composition in the Wimmera River differed most among reaches. This change in pattern was associated with the combined effects of decreased flow and longitudinal increases in salinity. In contrast, the fauna of the Glenelg River appeared to be resistant to the effects of the reduced flow season, owing to limited decline in water quality despite lower river discharge. 5. As salinisation and poor water quality in the Wimmera River result from human activities in the catchment, these results support the idea that human impacts on rivers can change macroinvertebrate scaling patterns and exacerbate the effects of drought beyond the tolerance of many riverine macroinvertebrates.