Summary1. Water withdrawal for irrigated agriculture is one of the leading uses of freshwater resources in the world; however, effects of low flow disturbances on lotic ecosystems are poorly understood. We studied an intensively managed agricultural catchment to determine: (i) how macroinvertebrate assemblages and environmental variables respond to water withdrawals of varying magnitude and duration; (ii) what environmental variables are associated with macroinvertebrate responses and (iii) the resiliency of macroinvertebrate communities to irrigation water withdrawals.2. We sampled above and below four irrigation diversions that create a gradient of increasing water withdrawal from upstream to downstream (i.e. 0%, 22%, 87%, 90% and 97% water withdrawn) along a 36 km river section. Three reaches were sampled above and below each point of diversion from June to September 2004 and 2005, which represented average and drought water conditions respectively.3. Irrigation water withdrawals were associated with both direct and indirect changes to the physicochemical environment. Direct effects (e.g. decreased velocity, depth and wetted habitat) were approximately proportional to the amount of water withdrawn, while indirect effects (e.g. increased conductivity and temperature) occurred when water withdrawals exceeded 85% of ambient levels.4. Changes in macroinvertebrate communities were more strongly related to indirect than direct effects of irrigation water withdrawals. In an average water year, community changes were associated with interacting thresholds of reduced discharge and increased conductivity. During a drought year, community changes were related to the interacting thresholds of reduced discharge and increased temperature.5. Between years, macroinvertebrate responses differed with the magnitude and duration of low flow conditions. In 2004, high‐intensity, relatively short‐duration water withdrawals (<2 months) and alterations to the physicochemical environment changed the relative abundance of macroinvertebrate communities, while macroinvertebrate indices and proportional abundances of functional feeding groups remained unchanged. In contrast, discharge reductions exceeding 90% of ambient levels and temperatures above 30 °C from July to September 2005 were associated with shifts in community composition from a dominance of collector‐gatherer and filterer Ephemeroptera, Plecoptera and Trichoptera taxa to predatory insects, non‐insect taxa and scraping elmid beetles.6. On an annual basis macroinvertebrate communities appeared resilient to the impacts of water withdrawals following winter high flows. In contrast, recovery was not observed after discharge and physicochemical variables returned to predisturbance conditions for only one month.7. Irrigation water withdrawals appear to impact macroinvertebrates through indirect effects that intensify with the magnitude and duration of water withdrawals and annual water availability. Preserving environmental conditions within natural ranges of variability, especially during low water years, appears critical to mitigating adverse biological responses to water withdrawals.
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