According to the Texas Integrated Report, segments of the Mission and Aransas rivers, the two primary freshwater contributors to Copano Bay, have been identified as not suitable for contact recreation because of elevated fecal bacteria. These fecal bacteria come from various sources, including feral hogs, failing septic systems, avian and non-avian wildlife, and livestock just to name a few. To reduce bacteria to levels safe for contact recreation, TWRI has worked with local stakeholders to develop a Total  Maximum Daily Load (TMDL) and TMDL Implementation Plan (I-Plan) and is now working with stakeholders to implement these developed plans. TWRI also developed a Watershed Protection Plan that was accepted by EPA in September 2021.