Extensive use of the Amudarya river waters for irrigation has severely impacted semi-natural ecosystems along its course and in its delta region. Currently, new strategies are searched for multi-user and multi-objective water management to mitigate ecological and socio-economic deterioration. The GIS-based modeling framework, TUGAI, has been developed to support exploration of alternative water management strategies for the Amudarya river delta and to analyze their ecological implications. Available information of heterogeneous type and quality on resource availability and habitat demands of deltaic ecosystems has been integrated into a comprehensive tool by a hybrid approach. A multi-objective water allocation model, AmuEPIC, has been combined with simple, spatially-explicit statistical and rule-based models of landscape dynamics, AmuGIS, and an ecological assessment procedure based on a fuzzy habitat suitability index model for riverine Tugai forests, TugaiHSI. Users can develop scenarios of alternative water management strategies for a time period of up to 30 years and compare their ecological effects. The tool facilitates a first quick assessment of the response of the delta environment to water management measures in a problem-oriented way. It assists in structuring the problem of water allocation to the environment, facilitates analysis of tradeoffs and uncertainties, fosters discussion between stakeholders and supports a goal finding process. Results of scenario analysis demonstrate solutions to given management tasks, which can serve as goals for implementation of measures in reality. First testing results indicate that there is a potential for increase of water discharge for environmental needs, while, at the same time, providing irrigation and other water users with sufficient water.