Water abstraction for irrigation poses significant stress on aquatic ecosystems and fish populations. In arid regions of New Zealand water abstraction practices often cause drought-like events to occur on an annual basis, resulting in many wadeable streams becoming disconnected from larger mainstem rivers or lakes. To assess the impacts on fish populations, we studied juvenile trout movement and mortality during the low flow period in the Lindis River, Central Otago, over two years. This river has a naturalised MALF of 1.9 m3, but water abstraction results in a residual summer flow of ≤ 25% of the MALF for 75 – 100 days in each year. The movements of >1000 juvenile brown trout (age 0+ and 1+) were tracked over the summer low flow period using passive integrated transponder (PIT) tags. PIT tagging occurred as the river was subject to extreme low flow conditions, which resulted in 20 – 35% (c. 1 – 1.8 km) of the study reach drying up during the study period each season. Preliminary analysis indicates that annual low flow events under water abstraction resulted in the death of a large proportion of the trout population within six weeks. Increased predation pressure, due to reduced habitat cover, rather than environmental conditions is thought to be the primary cause. Hence, this study has both national and international relevance for arid areas, and rivers where water abstraction levels represent a high proportion of the MALF for extended periods each year.