Gravel pit lakes form when gravel deposits are excavated below the water table. We studied two fluvial gravel pit lakes called De Lange Vlieter (DLV Lake) and the Boschmolen Plas (BP Lake), in the Meuse River valley (The Netherlands). Water from the Meuse River is pumped only into the DLV Lake that is used for drinking water production. The mean values, the linear trends and seasonal patterns of time series data (2003–2014), of temperature, pH, nitrate, phosphate and sulphate were compared using one-way tests of variance and tests of differences. The effects of river water infiltration on DLV Lake are (1) a change in lake water temperature; (2) an increase in nitrate concentration (3) an increase in phosphate concentration and (4) a decrease in sulphate concentration. The effects of the air blowers in DLV Lake are (1) mixing of lake water; (2) decreasing pH in spring and summer (3) water oxygenation. Linear regression analysis shows an initially increasing nitrate concentration in DLV Lake that can be explained by the input of nitrate rich Meuse river water. Instead decreasing nitrate and phosphate concentrations in BP Lake and Meuse River reflect a diminished use of fertilizers. The gravel pit lake water temperature does not reflect climatic changes but the use of DLV Lake for artificial recharge has an impact on the seasonal and long-term trends in hydrochemistry. This poses a challenge to lake managers to find the right balance between reduction of eutrophication and accumulation of nutrients and sulphate.