The Environmetrics Task View contains information about using R to analyse ecological and environmental data. Importantly it includes a list of packages useful for hydrology.

I’ve extracted part of the task view here but please also check the original. Acknowledgements to Gavin Simpson.

- Package HydroMe estimates the parameters in infiltration and water retention models by curve-fitting method.
- hydroTSM is a package for management, analysis, interpolation and plotting of time series used in hydrology and related environmental sciences.
- hydroGOF is a package implementing both statistical and graphical goodness-of-fit measures between observed and simulated values, mainly oriented to be used during the calibration, validation, and application of hydrological/environmental models. Related packages are tiger, which allows temporally resolved groups of typical differences (errors) between two time series to be determined and visualized, and qualV which provides quantitative and qualitative criteria to compare models with data and to measure similarity of patterns
- hydroPSO is a model-independent global optimization tool for calibration of environmental and other real-world models that need to be executed from the system console.hydroPSO implements a state-of-the-art PSO (SPSO-2011 and SPSO-2007 capable), with several fine-tuning options. The package is parallel-capable, to alleviate the computational burden of complex models.
- EcoHydRology provides a flexible foundation for scientists, engineers, and policy makers to base teaching exercises as well as for more applied use to model complex eco-hydrological interactions.
- topmodel is a set of hydrological functions including an R implementation of the hydrological model TOPMODEL, which is based on the 1995 FORTRAN version by Keith Beven. New functionality is being developed as part of the RHydro package on R-Forge.
- dynatopmodel is a native R implementation and enhancement of the Dynamic TOPMODEL, Beven and Freers’ (2001) extension to the semi-distributed hydrological model TOPMODEL (Beven and Kirkby, 1979).
- wasim provides tools for data processing and visualisation of results of the hydrological model WASIM-ETH
- The nsRFA package provides collection of statistical tools for objective (non-supervised) applications of the Regional Frequency Analysis methods in hydrology.
- The boussinesq package is a collection of functions implementing the one-dimensional Boussinesq Equation (ground-water).
- rtop is a package for geostatistical interpolation of data with irregular spatial support such as runoff related data or data from administrative units.