Maintenance of the natural flow regime is essential for continued wetland integrity; however, the flow regime is greatly influenced by both natural and anthropogenic forces. Wetlands may be particularly susceptible to altered flow regimes as they are directly impacted by water flows at a variety of time scales. In Puerto Rico, contemporary water management is decreasing freshwater recharge to wetlands and contributes to the salinization of important coastal wetlands as sea levels rise. Further, downscaled climate models predict an increase in drought frequency, intensity, and duration by mid-century. Conflicts over water allocation seem imminent between human and ecological needs. Current minimum flow policies are insufficient given the complexities of ecosystem processes and the changes in precipitation patterns and sea level rise that are expected in the future. Improved flow policies need to be established that reflect the functional relationships between specific representative ecological resources and components of the natural flow regime across all relevant time scales. Similarly, flow policies need to be developed within a landscape scale to implicitly address the socio-ecological trade-offs as well as the complexities of water management. Multi-disciplinary collaborations will be essential for increasing our resiliency to anticipated future changes.