Water quality forecasts are vital to determining limitations for point source waste loads and diffuse or nonpoint source loads required to meet water quality standards in streams, lakes, and estuaries. Only mechanistic water quality modeling is widely applicable for forecasting. Although surface water quality modeling has a sound interdisciplinary scientific basis, the use of these analysis tools are limited in regulatory and resource decision making by a lack of a professional consensus defining model application protocols. To analyze water quality problems, (i) the uses for a water body must be evaluated, (ii) models must be calibrated and tested to relate impaired water quality to the waste sources, (iii) a formal uncertainty analysis must define a margin of safety to protect human and ecological health, and (iv) when necessary, an economic analysis must be performed to determine if the designated uses are reasonably achievable.