1. Natural flow regimes play important roles in maintaining the ecological integrity and diversity of aquatic ecosystems. Wildlife has adapted over time to the natural dynamics of their environment, including changes in flow regimes. Changes in flow, including changes in magnitude, frequency, duration, timing and rate of change, may affect the physical characteristics of aquatic habitats, access to habitats, food availability, population dynamics and community composition.2. Given the importance of natural flow regimes for fish, it is necessary to understand the extent to which natural flow regimes alter fish abundance and diversity. Here we present a protocol for a systematic review that will estimate how fish abundance and diversity are affected by natural variation (resulting from climatic variability and broad-scale drivers such as climate-induced change) in flow.3. This systematic review will use evidence published before 2016 that was identified in a recent systematic mapping exercise on the broader topic of flow regime change impacts (both natural and anthropogenic) on direct outcomes of freshwater or estuarine fish productivity. An updated English language search will be performed using six bibliographic databases, Google Scholar and networking tools to include commercially published and grey literature that has been published after 2016. Eligibility screening will be conducted at two stages: title and abstract, and full-text. We will include all studies that evaluate the effect of natural changes in flow magnitude on fish abundance (broadly defined to also capture density and biomass metrics) and species diversity (broadly defined to also capture species richness and composition metrics). Any freshwater or estuarine fish species in temperate regions will be considered. 4. Included eligible studies will be assessed for study validity. We will extract information on study characteristics, intervention/comparator details, measured outcomesThis is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.