AQUATOX
EPA's aquatic ecosystem model — fate and ecological effects of nutrients, toxics and stressors together.
The classic river water-quality model — DO, nutrients and algae along a 1D stream network.
QUAL2K, by Steve Chapra and colleagues, modernised the venerable QUAL2E framework for steady-flow river water quality: dissolved oxygen sag, BOD, nutrient cycling, algae, pH and pathogens along a one-dimensional river, with diel temperature and light. Its transparent, spreadsheet-adjacent implementation made it the standard teaching and TMDL screening model for a generation.
Development has largely wound down (the QUAL2Kw fork from Washington State Ecology added auto-calibration and continued longer), but the methods remain textbook-standard, and for a steady low-flow waste-load allocation it still does the job it always did.
Other water quality & environmental tools covering similar workflow stages.
EPA's aquatic ecosystem model — fate and ecological effects of nutrients, toxics and stressors together.
EPA's watershed assessment suite — HSPF continuous watershed-quality modelling with GIS and data access built in.
The standard 2D reservoir and stratified-river water-quality model — temperature, DO and eutrophication.
Open-source 3D hydrodynamics and water quality — the EFDC lineage modernised, with a commercial GUI option.
USGS R package for long-term water-quality and streamflow trends — home of the WRTDS method.
EPA's Water Quality Analysis Simulation Program — eutrophication, toxics and sediment in rivers and estuaries.