An inexact rough-interval fuzzy linear programming (IRFLP) method is developed for agricultural irrigation systems to generate conjunctive water allocation strategies. The concept of “rough interval” is introduced in the modeling framework to represent dual-uncertain parameters. After the modeling formulation, an agricultural water allocation management system is provided to demonstrate the applicability of the developed method. The results show that reasonable solutions and allocation strategies are obtained. Based on the analysis of alternatives obtained from different scenarios, the significant impact of dual uncertainties existing in the system is specified. Comparisons between the results from IRFLP and interval-valued fuzzy linear programming are also conducted. The obtained rough-interval solutions correspond to the management strategies under both normal and special system conditions, and thus more conveniences would be provided for decision makers. Compared to the previous modeling efforts, the proposed IRFLP shows uniqueness in addressing the interaction between dual intervals of highly uncertain parameters, as well as their joint impact on the system.