The interlinkages between water for irrigation and for fish habitat are complex. This is particularly true in the Stung Chinit, a tributary to one of the most robust fisheries in the world, where livelihoods rely heavily on rice production and fishing and there is pressure to increase rice production with increased irrigation. This study assesses the tradeoffs between various management options and irrigation strategies in the Stung Chinit watershed under multiple projections of climate change. Due to the relative demands for instream flows and rice, if dry season rice is widely promoted, flows will be severely impacted. However, implementing a flow requirement protects these flows, while only causing minor shortages to rice when planted once or twice per year. These shortages may be alleviated with improved cooperation, management and shifting rice irrigation practices. While climate change will lead to warming temperatures and potentially higher demands for irrigation, the larger threat to rice and ecosystems appears to be water management (or lack thereof). This study suggests that there is sufficient water in the system to expand the irrigated area by 10%, grow rice twice per year and protect downstream flows under climate change; however, well-coordinated management is required to achieve this.