The paper analyzes modern trends in the development and use of software systems for three-dimensional hydrogeological modeling. It provides an analytical overview of most recent and widely used software products, their development process, the implemented models and the numerical methods applied. The study specifies a range of typical tasks addressed by Russian nuclear industry requiring the development of numerical geofiltration and geomigration models. To demonstrate the use of modern computational technologies, studied was the case involving calculations in the GeRa software package performed for LRW DDF. The paper identifies the trends for further software evolution taking into account the Russian needs in the development of near-surface and deep RW disposal facilities, decommissioning, as well as the accumulated experience in the operation of RW storage facilities and global trends in the code development.