I don't know of any drop-in replacements, but R has more than enough facilities to do anything needed for water quality simulation.
If I were magically restored to myself of 50 years ago as a young water quality planner and had today's tools, here's what I might start with.
If I planned to work with a lot of data (say 10^4 observations), I'd set up a postgres database because it has good support for spatial objects. (Such as watersheds, jurisdictions, measuring stations, stream courses, etc.) The {sf} package can read from a postgres database into a data frame, and plotting spatial objects in that format is easy and flexible using {ggplot2}.
For other water resources related packages, see the CRAN Taskview on hydrology.