Agriculture water use has been a major demand in the Colorado River basin. With future climate change impact, the availability of irrigation water will become even more critical in the basin. In this study, we used a coupled agent-based model (ABM)-RiverWare model to investigate farmers’ irrigation decision and its impact on water resource availability under future climate conditions in the San Juan River Basin, a major tributary of the Colorado River. The ABM-RiverWare model was calibrated with the historical irrigated area and streamflow data at the basin outlet. The ABM component in this coupled model allows farmers to adjust their annual irrigation decision based on their experience and the information of winter precipitation which is affected by future climate. We used five GCM model projections (IPSL-CM5A-LR, CanESM2, IPSL-CM5B-LR, CanESM2, HadGEM2-ES, and MIROC-ESM) with RCP8.5 scenarios for the study. Indices like reservoir storage, water shortage, instream flow requirements, and annual transboundary water are selected to quantify climate change impact on water resource availability. Modeling results show that water resources availability of the basin decreased, compared to historical conditions since 1) the annual flow violation days for instream flow requirements increased, 2) annual transboundary water diversion decreased, and 3) annual water shortages increased. Modeling results also suggest that farmers tend to decrease their irrigation area under future climate conditions as an adaptive management action to mitigate climate change impacts.