No attempt is made in either WEAP or QUAL2K to model water quality in reservoirs and lakes, due to uncertainties in vertical and longitudinal stratification and other complex processes. Additionally, QUAL2K does not allow for operable reservoirs whose storage can vary over time. (It does include sharp-crested weirs, but these are simple structures that are not operated.) For these reasons, when modeling water quality on a river with a reservoir, you might want to consider modeling it in two sections -- above the reservoir and below the reservoir.
Because QUAL2K does not consider reservoir storage and its effects on water quality, outflow concentrations are calculated simply as the weighted average of the inflows in a single time step, as described in Simple Mixing. Inflows include inflows from upstream and demand site and wastewater treatment plant return flows into the reservoir; outflows include outflows to downstream, evaporation and withdrawal by demand sites. A net decrease in storage is considered to be an inflow; a net increase in storage is an outflow. For purposes of mixing, the water quality concentration of the "inflow" from a decrease in storage is assumed to be the water quality flowing out of the reservoir from the previous time step.
Here is the simple mass balance equation (inflow = outflow):
UpstreamInflowRes + 
DSReturnFlowDS,Res +
TPReturnFlowTP,Res +
StorageDecreaseRes
=
DownstreamOutflowRes + EvaporationRes
+ TransLinkInflowRes,DS +
StorageIncreaseRes