The article discusses the application of FreezeThaw75 module, developed by one of the authors to calculate heat and mass transfer taking into account water–ice and ice–water–water phase transitions. Numerical simulations are compared with the analytical solution and other software codes. The module was tested at one of the injection sites in Daldino-Alakitskii district of Yakutia. FreezeThaw75 module was developed in relation to Feflow v7.4–7.5 model environment. The module was tested on a model of brine injection into frozen rocks. The model simultaneously takes into account the movement of groundwater flow, heat and mass transfer and phase transitions. A feature of the calculations in the developed model is the consideration of large injected volumes of highly mineralized brines.It influences the degradation of permafrost and takes into account the cryohydrogeological conditions of the site. Brines are injected into permafrost rocks with a high absorption capacity especially in areas confined to zones of tectonic disturbances. The developed module can adjust the predicted potential of the operated injection sites. It can also act as an additional element of control over the injection process and the formation of an artificial aquifer in the permafrost rocks.