The application of the lake model FLake to represent the effect of lakes in numerical weather prediction (NWP) and climate models is discussed. As a lake parameterisation scheme FLake is implemented into the limited-area NWP model COSMO. Results from a numerical experiment with the coupled COSMO-FLake system, including the complete COSMO-model data assimilation cycle, indicate a good performance with respect to the lake surface temperature and to the freeze-up of lakes and the ice break-up. The use of FLake removes a significant overestimation of the lake surface temperature during winter that is typical of the routine COSMO sea surface temperature analysis. Some challenging issues are discussed, such as the development of external-parameter fields and the lake temperature spin-up following a cold start of FLake in an NWP or climate model.