Benthic invertebrates support fish populations, reflect the health and resilience of the river ecosystem, and constitute most of the diversity of a river’s fauna. During the summer irrigation season, >50% of discharge may be abstracted from some Otago river catchments, with water diverted to pastures for irrigation. This seasonal reduction in river flow changes the availability and suitability of habitat for invertebrates. The aim of this study was to quantify the effect of seasonal water abstraction on benthic invertebrates along the Manuherikia River in Central Otago, a river currently subject to a minimum flow setting process being undertaken by the Otago Regional Council. Benthic macroinvertebrates, along with habitat variables, were sampled at three water diversions. Samples were collected from upstream (control sites) and downstream (impact sites) of diversions late in the irrigation season low-flow period (March), and after irrigation ceased and natural flow resumed in May and again in June 2019. Sampled invertebrates have been identified to the lowest practical taxonomic level. Preliminary results of total fixed counts show that invertebrate densities were lower downstream of takes in all seasons, and species richness and diversity are affected by water diversions. Recolonising invertebrate communities at banks are also affected by water abstraction. Impacts of abstraction were most severe during the irrigation season, but persisted for several months after natural flow resumed.