In this paper, two fuzzy cooperative games are utilized for modeling equitable and efficient water allocation among water users in both inter-basin and intra-basin water allocation problems. The proposed all-inclusive water allocation approach consists of three main steps, following Sadegh et al. (Water Resour Manage 24(12):2991–2310, 2010). In the first step, an initial water allocation is carried out using an optimization model taking into account an equity criterion. In the second step, the water users form crisp coalitions with fuzzy characteristic functions to increase the total net benefit of the system and also their own benefits. In the methodology used in this step, the water users do not need to have exact information about their payoffs and they can evaluate their payoffs as fuzzy numbers. In the second step, based on the Hukuhara difference of fuzzy numbers, optimum water allocation strategies are determined using a game with fuzzy characteristic function. In the third step, we applied another methodology which considers a class of fuzzy games with fuzzy characteristic functions and also fuzzy coalitions for water allocation. The methodology of this step is on the basis of the Hukuhara difference and the Choquet integral. The usefulness of the mentioned methodologies is studied by applying them to three defined real life scenarios in a case study of water allocation in Iran. The results showed that the proposed methodologies are professionally appropriate to real-world uncertain problems of equitable and economic inter-basin and intra-basin water resources allocations.