1. DataretrievalThis R package is designed to obtain USGS or EPA water quality sample data, streamflow data, and metadata directly from web services. See: http://usgs-r.github.io/dataRetrieval/
2. EgretciA bootstrap method for estimating uncertainty of water quality trends
3. nhdplusToolsSee official repository at: https://code.usgs.gov/water/nhdplusTools
4. EflowStatsCalculates Hydrologic Indicator stats and fundamental properties of daily streamflow for a given set of data
5. geoknifeR tools for geo-web processing of gridded data via the Geo Data Portal. geoknife slices up gridded data according to overlap with irregular features, such as watersheds, lakes, points, etc.
6. USGSHydroToolsCompilation of tools to aid in hydrologic and water quality analysis.
7. EGRETAn R-package for the analysis of long-term changes in water quality and streamflow, including the water-quality method Weighted Regressions on Time, Discharge, and Season (WRTDS). http://usgs-r.github.io/EGRET/
8. ncdfgeomNetCDF-CF Geometry and Timeseries Tools for R: https://code.usgs.gov/water/ncdfgeom
9. smwrGraphsMoved to: https://code.usgs.gov/water/analysis-tools/smwrGraphs
10. RainmakerRepo being permanently moved to: https://code.usgs.gov/water/analysis-tools/Rainmaker
11. streamMetabolizerstreamMetabolizer uses inverse modeling to estimate aquatic metabolism (photosynthesis and respiration) from time series data on dissolved oxygen, water temperature, depth, and light.