To fill the knowledge gap about the functioning of the lake–river system subjected to restoration treatments, two tributaries, a shallow, restored lake and its outflow, were examined. The quality of water inflows, lake and outflow was compared before (BR), during sustainable (SR, deep water aeration, phosphorus inactivation and biomanipulation for 3 years) and limited lake restoration (LR, only aeration for 2 years). Physico-chemical parameters were analysed monthly at five stations. The nutrient concentrations at the inflows decreased over the years due to the improvement of water and sewage management in the catchment (in Mielcuch from 18.0 to 8.0 mgN L−1 and 1.0 to 0.6 mgP L−1). The decline at the outflow was the result of a better quality of water at the tributaries and SR in the lake. During LR, decrease of phosphorus concentration still occurred (0.11 mgP L−1), but nitrogen concentration slightly increased (3.9 mgN L−1). Although the outflowing waters still transported a high content of chlorophyll a and suspended solids during SR, their amount was lower (34.5 μg L−1 and 17 mg L−1, respectively) than that during BR and LR. During restoration, it is significant to monitor the water quality not only in the lake but also at the outflow. The slow deterioration of water quality at the outflow indicated that introducing changes in the applied restoration methods must be done carefully because the previously achieved effect may be lost. Hence, restoration of the upstream lake and good quality of its tributaries are of great importance for water bodies located downstream.