The watershed’s ecosystem is under stress from rapid urban development, land use changes, incompatible agricultural practices, wastewater management and water supply practices, and resource extraction activities. Many communities in the watershed are experiencing periodic flooding which is only expected to worsen as development continues. The major problems are quality of aquatic habitat and water supply. Aquatic habitat problems stem from riparian buffer alteration, bank erosion, sedimentation, nutrient loading, and low dissolved oxygen. Water supply issues are controversial because a high quality and quantity water flow is essential for both supporting rare aquatic species and meeting the basin’s growing municipal water demands.