Many waterbodies around the world are adversely impacted by harmful algal blooms (HABs). One primary driver of these blooms is often high concentrations of anthropogenic phosphorus loading. The phosphorus mitigation plans require accurate information on nutrient sources and transport, to and through water bodies, including the stream network. Diffuse sources, are particularly difficult to quantify due to the cost of in situ monitoring, and is often supplemented using various water quality models. SWAT, a comprehensive watershed-scale model, is widely used to assess and improve downstream water quality using QUAL2E equations. EPA developed QUAL2E can model phytoplankton growth but has a limited capacity to model benthic algae. Although SWAT requires a lesser number of parameters while simulating water quality outputs, unlike, HSPF, INCA, SPARROW, WASP, and MIKE-SHE, the water quality algorithm within SWAT needs modifications for simulating phosphorus legacy within the waterbodies. This study reviews the existing water quality models to improve the water quality algorithm within SWAT. Most of the water quality models can simulate processes, including the proliferation of fixed and floating algal biomass and phosphorus cycling (QUAL2E/K, WASP, HSPF). Some water quality models are better in simulating the time-dependent factors, such as light attenuation, form and concentration of nutrients, and water temperature (HSPF, INCA). There are a few water quality algorithms that can simulate both horizontal stream flow and shallow flow (SHETRAN, INCA). Both horizontal and shallow flow takes into account the anisotropy and variable biogeochemistry impacts on the turbulence of water, thus, the water quality. Some water quality models simulate the non-linear relationship between nutrient concentration and discharge timing and magnitude (SPARROW). There are some commercialized models like MIKE-SHE that simulate reasonably good results, but the water quality algorithm/equation/process is not publically available. Our review of the existing water quality models will help in identifying, modifying, and implementing the SWAT source code revisions required to improve and mitigate water quality degradation from a finer spatial scale, including small ditches and streams, to the large-scaled watershed over time.