Allocating finite water resources between different water uses is always a challenging task. Searching for a solution which satisfies the water needs (requirements) of all water users without compromising the water requirements of river ecosystems calls for analyzing different water management options and their expected consequences. Water management balances are usually used for comparison of water resources with the needs of water users. When aquatic and water dependent ecosystems are considered in a similar manner as other users, searching for the optimum water resources allocation, without neglecting requirements of the natural environment, is possible. This paper describes basic modeling assumptions and methodological solutions, which allow for taking into account some tasks related to the protection of aquatic and water dependent ecosystems. The water balance model, developed for a catchment comprising the Warta Mouth National Park, was applied to find out whether supplying adequate amounts of water for conservation (or restoration) of wet meadows and wetland habitats in the area is possible, while still satisfying the demands of other water users.