In regulated rivers, managers must evaluate competing flow release scenarios that attempt to balance both human and natural needs. Meeting these natural flow needs is complex due to the myriad of interacting physical and hydrological factors that affect ecosystems. Tools that synthesize the voluminous scientific data and models on these factors will facilitate management of these systems. Here, we present the Riverine Environmental Flow Decision Support System (REFDSS), a tool that enables evaluation of competing flow scenarios and other variables on instream habitat. We developed a REFDSS for the Upper Delaware River, USA, a system that is regulated by three headwater reservoirs. This version of the REFDSS has the ability to integrate any set of spatially explicit data and synthesizes modeled discharge for three competing management scenarios, flow-specific 2-D hydrodynamic modeled estimates of local hydrologic conditions (e.g., depth, velocity, shear stress, etc.) at a fine pixel-scale (1 m2), and habitat suitability criteria (HSC) for a variety of taxa. It contains all individual model outputs, computationally integrates these data, and outputs the amount of potentially available habitat for a suite of species of interest under each flow release scenario. Users have the flexibility to change the time period of interest and vary the HSC. The REFDSS was developed to enable side-by-side evaluation of different flow management scenarios and their effects on potential habitat availability, allowing managers to make informed decisions on the best flow scenarios. An exercise comparing two alternative flow scenarios to a baseline scenario for several key species is presented. The Upper Delaware REFDSS was robust to minor changes in HSC (± 10 %). The general REFDSS platform was developed as a user-friendly Windows desktop application that was designed to include other potential parameters of interest (e.g., temperature) and for transferability to other riverine systems.