The formation of ice cover on lakes alters heat and energy transfer with the water column. The fraction of surface area covered by ice and the timing of ice‐on and ice‐off therefore affects hydrodynamics and the seasonal development of stratification and related ecosystem processes. Multi‐year model simulations of temperate lake ecosystems that freeze partially or completely therefore require simulation of the formation and duration of ice cover. Here we present a multi‐year hydrodynamic simulation of an alpine lake with complex morphology (Lower Lake Constance, LLC) using the three‐dimensional (3D) model AEM3D over a period of 9 years. LLC is subdivided into three basins (Gnadensee, Zeller See and Rheinsee) which differ in depth, morphological features, hydrodynamic conditions, and ice cover phenology and thickness. Model results were validated with field observations and additional information on ice cover derived from a citizen science approach using information from social media. The model reproduced the occurrence of thin ice as well as its inter‐annual variability and differentiated the frequency and extent of ice cover between the three sub‐basins. It captured that full ice cover occurs almost each winter in Gnadensee, but only rarely in Zeller See and Rheinsee. The results indicate that the 3D model AEM3D is suitable for simulating long‐term dynamics of thin ice cover in lakes with complex morphology and inter‐annual changes in spatially heterogeneous ice cover.