Understanding farmers’ decision-making on crop choices and water use is essential for agricultural water resource management. However, previous studies have limited understanding of how farmers’ behavioral characteristics affect their crop choices and water use in agricultural systems. To fill this research gap, in this study we develop an agent-based model (ABM) that incorporates two types of behavioral characteristics (i.e., perception to the uncertainty in future crop prices, planting cost and precipitation, and tolerance to the variation of crop profits) to investigate their effects on crop choices and water use under the influence of water management policies. The ABM is applied to the Heihe River Basin (HRB), an arid endorheic river basin in northwestern China as a demonstration. The modeling results show that farmers with adventurous perceptions and high tolerance level (Type I) tend to choose high-profit crops. They are more likely to have a single-crop pattern with high crop profits and high water consumption. In comparison, farmers with cautious perceptions and low tolerance level (Type II) prefer steady profit crops. They typically pay more attention to the variation of crop profits, resulting in a mixed crop pattern with low crop profits and low water consumption. In addition, the two types of farmers exhibit varied responses to water management policies. The Type I farmers are more sensitive to the changes in the volume of water permits and irrigation efficiency, and as a result, are more sensitive to the changes of water management policies than the Type II farmers do. We also find that the effects of farmers’ behavioral characteristics vary at the irrigation district level, county level and entire study area level. These findings emphasize the importance of incorporating farmers’ behavioral characteristics into crop choice and water use models. The modeling result could provide policy implications for designing location-based water management policies that account for the heterogeneity in farmers’ behavioral characteristics and responses to water policies.