The fringes of lake shorelines, known as littoral zones, are highly productive regions that host dense aquatic vegetation and contribute substantially to methane emissions. Despite their importance, littoral zones are often underrepresented in lake greenhouse gas budgets, partly due to their spatial complexity and the limited understanding of the physical and biogeochemical processes that link them to pelagic waters. This project aims to develop a coupled three-dimensional hydrodynamic and biogeochemical modelling framework to quantify lateral and vertical transport processes between the littoral and pelagic zones of Lake Erken, with a particular focus on methane dynamics. TELEMAC-3D has been selected as the core hydrodynamic model and will be coupled with the AED2 biogeochemical module. Meteorological and geospatial data will be collected from a combination of field measurements, in situ measurements and remote sensing sources. Computational meshes have been generated for this project with a flexible structure that allows for a finer resolution in the littoral zone. This improves the representation of littoral areas while maintaining computational efficiency. The littoral zone will be defined based on the depth at which submerged aquatic plants can grow in the lake. Model setup and calibration will focus on reproducing the thermal structure, mixing dynamics and circulation patterns that influence littoral–pelagic exchange. Subsequent simulations will quantify tracer and greenhouse gas transport across this interface, supported by velocity field measurements collected in the lake. The resulting coupled model is expected to advance understanding of process interactions in littoral zones and improve estimates of their contribution to whole-lake greenhouse gas cycling.