Lake Banyoles is a multibasin lake dominated by groundwater derived inflows. It is composed of three major basins, two of them being meromictic. The relatively warm and saline groundwater inflows, together with the basin morphometry, give rise to characteristic thermal structures in each basin, with different thermocline levels and temperature inversions distinguishing the basins. A one-dimensional lake mixing model has been adapted to include the form of mixing associated with the groundwater inflows, and the results are compared with data collected from the lake.