Raoul Collenteur from the University of Graz provides a list of open source Python projects for hydrogeological applications. This list includes tools and applications for the following topics:
A interesting overview of R packages in hydro(geo)logy can be found at CRAN Hydrological Data and Modeling.
Also, the application and existing useful R tools in hydrology are outlined in several review articles:
These articles provide an overview of a typical hydrologic workflow based on reproducible principles and packages for hydrometeorological data retrieval, spatial analysis, hydrologic modeling, statistics, and the design of static and dynamic visualizations and documents.