There is a computer decision support system (CDSS) for urbanization of the northern part of the Volga-Akhtuba floodplain. This system includes subsystems of cognitive and game-theoretic analysis, geoinformation and hydrodynamic simulations. The paper presents the cognitive graph, two-level and three-level models of hierarchical games for the cases of uncontrolled and controlled development of the problem situation. We described the quantitative analysis of the effects of different strategies for the spatial distribution of the urbanized territories. For this reason we conducted the territory zoning according to the level of negative consequences of urbanization for various agents. In addition, we found an analytical solution for games with the linear dependence of the average flooded area on the urbanized area. We numerically computed a game equilibrium for dependences derived from the imitational geoinformation and hydrodynamic modeling of flooding. As the result, we showed that the transition to the three-level management system and the implementation of an optimal urbanization strategy minimize its negative consequences.