BASINS
EPA's watershed assessment suite — HSPF continuous watershed-quality modelling with GIS and data access built in.
EPA's aquatic ecosystem model — fate and ecological effects of nutrients, toxics and stressors together.
by US EPA
AQUATOX is unusual: it simulates the aquatic ecosystem itself — algae, macrophytes, invertebrates, fish — together with the fate of nutrients and organic toxics, so management scenarios propagate from chemistry to biology. Questions like "what does a 30% nutrient reduction do to the fish community" are its niche.
It is free EPA software with a real learning curve and a parameter appetite to match its ambition. Active development has slowed, but it remains the most complete free ecosystem-effects model available for freshwater risk assessments.
Other water quality & environmental tools covering similar workflow stages.
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.
The classic river water-quality model — DO, nutrients and algae along a 1D stream network.
EPA's Water Quality Analysis Simulation Program — eutrophication, toxics and sediment in rivers and estuaries.