Groundwater plays a vital role to both provide drinking water and to keep ecosystems healthy and functioning. Changes to groundwater flow affect reaction times and solute concentrations. In northern regions thawing permafrost is altering groundwater flow, storage, and solute transport. In particular, thawing permafrost increases hydraulic connectivity, boosting groundwater discharge and mobilizing organic matter, metals, and other contaminants that were previously immobile. Currently there is no existing models which incorporates both freeze-thaw cycles and non-conservative solute transport. The community of Whatì in the Northwest Territories, located in discontinuous permafrost, seeks to understand how groundwater in its bog-fen wetland complex connects to surrounding aquatic ecosystems. This study aims to develop a groundwater model for a fen in Whatì that couples heat flow, groundwater movement, and reactive solute transport. This will help predict how the system responds to permafrost degradation and climate warming. The modelling approach uses two tools, the SHAW model will simulate one-dimensional heat, water, and solute transfer using local climate data. Its outputs ground temperature and surface water flux which will be applied as boundary conditions in a three-dimensional FEFLOW model with the piFreeze freeze–thaw plugin. FEFLOW will simulate groundwater flow and solute active transport, establishing baseline predictions for groundwater quantity and quality. The method adapts a successful earlier wetland study, modifying its SHAW and FEFLOW frameworks to include reactive solute transport. The completed model will be the first to integrate permafrost, groundwater flow, and reactive solute transport, providing valuable insight into future drinking-water security and ecosystem health.