The focus of this work was to develop a general methodology for modeling water quality in coastal waterbodies. The methods were developed in the context of modeling bacterial total maximum daily loads (TMDLs), but the general approach is applicable to a wide variety of pollutants. The study area for this dissertation was the Copano Bay watershed, which is located on the Texas Gulf Coast. The developed approach combines simple modeling techniques, of the type recommended by state and national advisory groups, in a GIS (geographic information system) framework, resulting in a methodical, easily transferred approach. This work addresses coastal systems where water quality is a function of operations in non-tidal rivers, tidal rivers, and bays, combined with the effects of watershed contributions. An uncertainty analysis was done to quantify a subset of the variance in the modeled results. Outcomes from this work include modeling tools, a documented workflow for modeling water quality in coastal watersheds, procedures to quantify the uncertainty associated with the developed approach, insight to the factors affecting water quality in the study area, and mean annual bacterial TMDLs for the impaired waterbodies of the Copano Bay watershed. / text