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In especially arid/semi-arid regions, wetlands are steadily destroyed or converted into other forms of land use due mainly to population and socio-economic growth. The accurate estimation of catchment hydrological processes is therefore vital not only for sustainable land/water resources management in these regions, but also for the adequate preservation of wetland ecosystems. In this study, distributed recharge, runoff and evapotranspiration (ET) are simulated for the wetland-based ecosystem of Western Jilin using WetSpass (Water and Energy Transfer between Soil, Plants and the Atmosphere under quasi-Steady-State), extended with MODFLOW. Comparisons of hydrophysiographic conditions of 1930 and 2000 show good agreements between the model-simulated fluxes and long-term field-measurement data, all with R-2 above 0.8. About 21% of the wetlands have been converted into primarily farmlands. Water quality is also deteriorating due to land use change and accompanying increase in ET against decreasing recharge. While ET is highest for open water surfaces, it mostly originates from vegetated land surfaces. Recharge is not only highest, but also mainly originates from vegetated land surfaces. Similarly, runoff is highest and largely originates from bare land surfaces. Whereas ET is influenced mainly by land use, recharge and runoff are variously influenced by land use, soil type and topographic slope. Changes in the hydrophysiographic conditions pose a considerable threat to wetland ecosystems in the study area. As ET is the predominant mode of water loss, ET-limiting land/water resources management strategies are critical for environmental sustainability and for long-term restoration and conservation of the fragile wetland-based ecosystem. Copyright (C) 2009 John Wiley & Sons, Ltd.