Water shortages and nutrient pollution in a growing number of basins put human water security and aquatic biodiversity at risk. These challenges are harder to tackle in transboundary river basins. Transboundary river basin organizations (RBOs), which manage water based on hydrologic boundaries, and environmental flows are promoted as two solutions. While they show promise for resolving pressing water issues, an evaluation of their effectiveness is needed to determine the potential impact of their more widespread use. I address this need by asking: (1) What are the major governance factors and social processes to consider in developing a transboundary RBO that can affect water management at a basin scale given the current regulatory and political landscape; (2) Are transboundary RBOs effective in achieving two of the most prominent environmental objectives, managing low flows and nutrient loads, given their regulatory authority as well as their financial and technical capacity; (3) Does the Susquehanna River Basin Commission, a transboundary RBO, have sufficient policies and programs to effectively implement environmental flows and does their low flows policy affect low flows at the river basin scale? My results show: (1) Designing transboundary RBOs requires identification of gaps and opportunities, deliberation with all relevant players on functions, and a process to transition from the current regulatory landscape to one that includes a transboundary RBO. (2) Transboundary RBOs exhibited modest biophysical results, with more strength of evidence for low flows than for total nitrogen flux. Interviews revealed other benefits not captured by biophysical indicators and the importance of regulatory authority, financial capacity, and technical capacity. (3) The Susquehanna River Basin Commission is making a significant improvement in low flows, some progress towards the seasonal flows, and limited progress towards high flows. A concerted effort between all institutions with control over the flow regime is needed to fully implement environmental flow recommendations.