The Clean Water Act requires states to identify water bodies that do not meet water quality criteria for their designated use (human consumption, aquatic life support, recreational use, etc.) and develop total daily maximums loads (TMDLs) as a way to control pollutant influx to receiving bodies. Watershed scale models that tie anthropogenic, geochemical, and hydrologic activity to changes in chemical water quality are widely used to develop TMDLs and policy mechanisms to restore water quality. Current trends in water quality monitoring of streams and lakes have moved from chemical sampling (total nitrogen, total phosphorus, dissolved oxygen) to biological sampling due to the low resource requirement and the ability to capture long-term water quality of biological sampling. Many state agencies have integrated statewide biological monitoring programs as a way of monitoring water quality and aid in setting TMDLs. Our goal is develop an in-stream model that links best management practices to changes in biological profiles to help decision makers set numerical criteria for TMDLs and develop programs to improve water quality in impaired streams. In order to account for a range of water body impairments, three different watersheds will be modeled: non-impacted, slightly impacted, and severely impacted. The Soil and Water Assessment Tool (SWAT) will be used for hydrologic simulations and determining impacts of best management practices on water quality. It will be coupled with an in-stream macroinvertebrate model that will produce the population’s response to SWAT simulated constituents.