Data for: Mimicking functional elements of the natural flow regime promotes native fish recovery in a regulated river

Environmental flows are essential to the conservation of riverine biodiversity, and are increasingly designed to protect components of the flow regime that support critical ecosystem functions. Yet, few studies have quantified biological responses to individual components of environmental flows. We used multivariate autoregressive state-space (MARSS) models to analyze 25 years of fish assemblage data collected before and after court-ratified environmental flows were implemented in Putah Creek, a dammed stream in California, USA. We quantified functional components of the flow regime that have been identified for Mediterranean climate regions of western North America and identified changes in these components from before to after the environmental flow regime was implemented. Additionally, we compared these values to their predicted natural ranges and modeled the probability of native and non-native fish assemblages declining by > 80% (quasi-extinction risk) under alternative management scenarios spanning the observed range of flow conditions. We found that as individual functional flow metrics became more similar to the ranges expected under natural, unaltered conditions, the quasi-extinction risk for the native fish assemblage decreased. Three functional flow metrics that shifted towards natural ranges following environmental flow implementation, fall pulse flow magnitude, wet season timing, and dry season duration, each corresponded with a 40% or greater decrease in native assemblage quasi-extinction risk. However, decreased spring recession flows and greater dry season baseflows post-flow modification shifted these metrics further from their natural ranges, increasing quasi-extinction risk for the native assemblage. Flow management scenarios revealed that the non-native fish assemblage quasi-extinction risk increased as flow metrics became more natural and decreased under more altered flow conditions. Few functional flow metrics were restored to their natural ranges following environmental flow implementation, yet even the modest changes towards more natural flows were found to suppress non-native and benefit native fish assemblages. Our findings illustrate that mimicking functional components of the natural flow regime is an important tool for designing environmental flows to conserve freshwater biodiversity.