WEAP includes descriptive models of point source pollutant loadings that can simulate the impact of wastewater on receiving waters from demand sites and wastewater treatment plants. Water quality parameters that can be considered in WEAP include conservative substances, constituents that decay according to an exponential decay function, dissolved oxygen (DO) and biological oxygen demand (BOD) from point sources, and instream water temperature. These parameters are not modeled in reservoirs, though; all reservoir outflow concentrations must be entered as data.

In the first-order DO model, water quality is simulated in select rivers, chosen via the WEAP user interface. Mass balance equations are written for each stream segment of the selected rivers, with hydrologic inflows from rivers and groundwater sources automatically input to simulate the water balance and mixing of DO, BOD and other constituents along each reach. The river network is the same for the water resources and water quality simulations and assumes complete mixing.

First, all pollution loads into a river are calculated from demand site return flows, wastewater treatment plant return flows, groundwater inflows, headflows, upstream inflows, and other surface water inflows. WEAP assumes complete mixing of all inflows. As each constituent (other than conservative constituents) moves downstream, its decay is calculated.