Lakes can store water for long periods of time, which influences the transport of water and hydrologic tracers and changes catchment transit times downstream. However, the impact that the transit time of lakes has on catchment transit times has received little attention to date. We derived water and isotope mass balances for two lakes and examine the use of time‐variant transit time solutions with StorAge Selection functions to estimate the water ages of evaporation and lake outflows. We used the convolution of the StorAge Selection function transit time estimations with inflow transit times to estimate the transit times downstream of each lake. The lakes exhibited contrasting storage effects for discharge; with direct storage effects (newest water exiting during low flow) for a larger lake fed by a small catchment, and inverse storage effects (newest water exiting during high flow) for a smaller lake with a large catchment. The water and isotope mass balance yielded estimates of daily and annual evaporation fluxes, which were similar between the two lakes. The proposed framework is an effective tool to identify the effects of precipitation, surface inflow, and evaporation on the transit times for relatively small, shallow lakes, using a combination of water and isotope mass balance methods.