Cooperative game theory can be used for management of water resources in transboundary river basins. Applications of game theory which have been used for conflict analysis in water resources management include metagame analysis and graph models. These games are not considered classical game theory. These games allow strategies to evolve over time through repeated play and the players typically do not have communication prior to play. In cooperative game theory the players, or decision makers, have communication prior to the game and are allowed to make joint agreements. Cooperative games are considered non-zero-sum games where the costs and benefits of decisions are allocated to all players. Unlike metagames or graph models, the user must specify all possible strategy sequences that could occur. In a transboundary river basin setting, to generate the possible strategies, a water resources model is used to generate the payoffs from the sequence of strategies. These payoffs are then entered into a payoff matrix for calculations. In this paper, an application of cooperative game theory for the Syr Darya basin is presented.