The ice cover on lakes is one of the most influential factors in the lakes’ winter aquatic ecosystem. The paper presents a method for predicting ice coverage of lakes by means of multilayer perceptrons. This approach is based on historical data on the ice coverage of lakes taking Lake Onega as an example. The daily time series of ice coverage of Lake Onega for 2004–2017 was collected by means of satellite data analysis of snow and ice cover of the Northern Hemisphere. Input signals parameters for the multilayer perceptrons aimed at predicting ice coverage of lakes are based on the correlation analysis of this time series. The results of training of multilayer perceptrons showed that perceptrons with architectures of 3-2-1 within the Freeze-up phase (arithmetic mean of the mean square errors for training epoch