The aim of the special issue is to present new methods of handling lakes in the numerical weather prediction and climate models, and to use these methods to investigate two-way interactions between lakes and the atmosphere in a changing climate. The special issue will bring together specialists in several geophysical disciplines - climate research, boundary-layer meteorology, limnology, biogeochemistry, cryosphere research - focusing on lake-related processes. As an outcome, a significant advance is expected in our understanding of the role played by lake systems in atmosphere-hydrosphere interactions. The special issue arises from the "5th workshop on the parameterisation of lakes in numerical weather prediction and climate models", which was held from 16 to 19 October 2017 in Berlin. However, while the special issue was conceived during this meeting, it will not merely be a conference proceeding, but will instead aim to embody the most important advances within our research field during the past few years. The special issue will therefore be open for all submissions within its scope.