Using lake Stechlin in northeastern Germany as an example of a small groundwater-feed lake without surface inflows and outflows, we estimated the temporal scales and the variability ranges of the net groundwater contribution to the lake water budget. High-resolution water level measurements by a bottom-mounted pressure logger provided the background for the estimation of the total lake water budget. This method has demonstrated reliability for estimation of lake level variations during periods ranging from subdiurnal to perennial. The typical amplitudes of the synoptic-to-perennial variability characterizing the groundwater climate of lake Stechlin are estimated by comparing the two subsequent years 2006 and 2007; one of these years shows an extremely high, and the other an extremely low, annual precipitation–evaporation balance. The net groundwater flow, estimated as the difference between the total water budget and the precipitation–evaporation balance at the surface, revealed synoptic effects of lake water exfiltration into the groundwater aquifer following strong precipitation events. Perennial variations between wet and dry years superimposed seasonal oscillations. The probable origin of the latter is seasonality in the groundwater level on the watershed, although the exact amplitudes are subject to further quantification on account of seasonality in the evaporation estimation error. The results emphasize the non-stationary behaviour of groundwater flow on timescales shorter than climatic ones. The analysis yielded a net quantitative relationship between groundwater flow and water balance at the lake surface: The water level changes in the lake due to evaporation and precipitation are damped to 60% because of the lake–groundwater exchange by means of intermittent infiltration and exfiltration events. Assuming the remaining 40% of the surface water budget may potentially result in perennial water level variability, we estimated an effect of the precipitation decrease on the lake water budget as predicted by the regional climate scenarios for the next century. Copyright © 2012 John Wiley & Sons, Ltd.