Propagation of uncertainty in lake temperature models is studied using a vector state space method. The output uncertainty is defined as the result of deviations of the meteorological variables from their mean values. The analysis is applied to systems with correlated and uncorrelated meteorological variables. Surface water temperatures are strongly affected by uncertain meteorological forcing. Air temperatures and dew point temperature fluctuations have significant effect on lake temperature uncertainty. Ignoring correlation in meteorological variables underestimates uncertainties in lake temperature estimates. Long‐term average water temperature structure in lakes can be estimated by computer model simulation for just 1 year when results from a statistical analysis of meteorological variables are used as input. The analysis presents a useful alternative for the study of long‐term averages and variability of water temperature structures in lakes due to variable meteorological forcing.