In this research, a dual-inexact fuzzy stochastic programming (DIFSP) method was developed for supporting the planning of water and farmland use management system considering the non-point source pollution mitigation under uncertainty. The random boundary interval (RBI) was incorporated into DIFSP through integrating fuzzy linear programming (FLP) and chance-constrained programming (CCP) approaches within an interval linear programming (ILP) framework. This developed method could effectively tackle the uncertainties expressed as intervals and fuzzy sets. Moreover, the lower and upper bounds of RBI are continuous random variables, and the correlation existing between the lower and upper bounds can be tackled in RBI through the joint probability distribution function. And thus the subjectivity of decision making is greatly reduced, enhancing the stability and robustness of obtained solutions. The proposed method was then applied to solve a water and farmland use planning model (WFUPM) with non-point source pollution mitigation. The generated results could provide decision makers with detailed water supply–demand schemes involving diversified water-related activities under preferred satisfaction degrees. These useful solutions could allow more in-depth analyses of the trade-offs between humans and environment, as well as those between system optimality and reliability. In addition, comparative analyses on the solutions obtained from ICCP (Interval chance-constraints programming) and DIFSP demonstrated the higher application of this developed approach for supporting the water and farmland use system planning.