Escalating demands for water have led to substantial modifications of river systems in arid regions, which coupled with the widespread invasion of nonnative organisms, have increased the vulnerability of native aquatic species to extirpation. Whereas a number of studies have evaluated the role of modified flow regimes and nonnative species on native aquatic assemblages, few have been conducted where the compounding effects of modified flow regimes and established nonnatives do not confound interpretations, particularly at spatial and temporal scales that are relevant to conservation of species at a range-wide level. By evaluating a 19-year data set across six sites in the relatively unaltered upper Gila River basin, New Mexico, USA, we tested how natural flow regimes and presence of nonnative species affected long-term stability of native fish assemblages. Overall, we found that native fish density was greatest during a wet period at the beginning of our study and declined during a dry period near the end of the study. Nonnative fishes, particularly predators, generally responded in opposite directions to these climatic cycles. Our data suggested that chronic presence of nonnative fishes, coupled with naturally low flows reduced abundance of individual species and compromised persistence of native fish assemblages. We also found that a natural flow regime alone was unlikely to ensure persistence of native fish assemblages. Rather, active management that maintains natural flow regimes while concurrently suppressing or excluding nonnative fishes from remaining native fish strongholds is critical to conservation of native fish assemblages in a system, such as the upper Gila River drainage, with comparatively little anthropogenic modification.

The ubiquitous presence of nonnative fishes, both sport and nongame, within waters of the southwestern United States is the foremost factor preventing immediate conservation and recovery of imperiled native fishes. We present evidence that the two fishery types cannot be co‐managed in sympatry if natives are to persist. A dual responsibility of federal and state fish and wildlife agencies to manage both fishery types creates internal conflicts that typically are resolved in favor of nonnative sport fisheries, despite existence of the Endangered Species Act. We advocate designation of watersheds to be managed exclusively for one fishery type or the other, and implementation of an aggressive program to eliminate nonnatives in native‐designated waters and protect against their reinvasion. To mitigate institutional conflicts, agency infrastructures should be segregated to promote independent management of native fisheries and introduced sport fisheries. This approach can fulfill mandates of both the Endangered Species Act and the 1996 Fish and Wildlife Service policy on recreational fishing.

Motivation: We compiled a global database of long-term riverine fish surveys from 46 regional and national monitoring programmes and from individual academic research efforts, with which numerous basic and applied questions in ecology and global change research can be explored. Such spatially and temporally extensive datasets have been lacking for freshwater systems in comparison to terrestrial ones. Main types of variables contained: The database includes 11,386 time-series of riverine fish community catch data, including 646,270 species-specific abundance records, together with metadata related to the geographical location and sampling methodology of each time-series. Spatial location and grain: The database contains 11,072 unique sampling locations (stream reach), spanning 19 countries, five biogeographical realms and 402 hydrographical basins worldwide. Time period and grain: The database encompasses the period 1951-2019. Each timeseries is composed of a minimum of two yearly surveys (mean = 8 years) and represents a minimum time span of 10 years (mean = 19 years). Major taxa and level of measurement: The database includes 944 species of rayfinned fishes (Class Actinopterygii). Software format: csv. Main conclusion: Our collective effort provides the most comprehensive long-term community database of riverine fishes to date. This unique database should interest ecologists who seek to understand the impacts of human activities on riverine fish biodiversity and to model and predict how fish communities will respond to future environmental change. Together, we hope it will promote advances in macroecological research in the freshwater realm.

Summary 1. Fish assemblages and habitats were sampled annually at fixed sites in three tributaries of the Gila River catchment over a 21‐year span that included prolonged low‐ and high‐flow periods. Model selection was used to evaluate responses of seven native fishes with variable ecological traits (four small‐bodied cyprinids, one large‐bodied cyprinid, and two large‐bodied catostomids) to mean annual discharge and predacious non‐native fishes across the three sites. We also compared habitat use and overlap of native and non‐native fishes to identify potential for negative interactions among species. 2. Assemblage structure (species abundance and richness) and recruitment of native species was strongly and primarily affected by mean annual discharge and secondarily by location and densities of non‐native predators (mainly the centrarchid Micropterus dolomieui). 3. Densities of age‐0 catostomids and small‐bodied cyprinids were positively associated with discharge, and this pattern was strongest in the tributary with the lowest densities of non‐native predators. Absence or extreme low abundance of natives during low‐flow years was most pronounced at the sites where non‐native predators were comparatively common. Densities of adults of large‐bodied native species also varied by site, but often were positively associated with densities of non‐native predators. 4. Spatially variable responses of native fish assemblages indicated that the persistence of native fishes could be jeopardized if key habitats were lost or flow regimes unnaturally altered, particularly during low‐flow conditions when recruitment of native fishes is low and predation by non‐natives is high. Large‐bodied species may be less vulnerable to multiple years of poor conditions because adults are able to avoid predation by non‐natives and thus can rely on occasional high discharge years for successful recruitment. 5. As in other arid‐land streams, native fish assemblages of the Gila River Basin continue to decline. Our results indicate that conservation requires specific knowledge and consideration of physical influences as well as life‐history attributes of native and non‐native fishes.

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