This dissertation presents an integrated modeling system for multi-objective management of life-supporting ecosystem services, which are frequently impaired by a wide variety of natural and anthropogenic activities in watersheds. The research work specifically focuses on maintaining water quality in streams and rivers through evolution of agricultural landscapes. The development of this integrated modeling system involves coupling of multi-objective evolutionary algorithms with physically-based, distributed hydrologic model. As part of this research effort, automatic calibration tools for the distributed hydrologic model are developed, and sensitivity and uncertainty associated with the hydrologic modeling are investigated. In addition, the use of artificial intelligence techniques is explored to reduce the computational demand of the integrated modeling system.