The Intergovernmental Panel on Climate Change (IPCC) predicts increases in global average surface temperature from 1.1 to 6.4 °C for the year 2100. Here, we focus on the impact of climate warming on eutrophic shallow lakes in the Netherlands, using three representative lakes that cover the full range of lake sizes and depths. In these lakes, temperature has been shown to be the main determinant of hatching and growth of young-of-the-year fish. Because records of water temperature of our study lakes are incomplete, we applied an existing model to predict water temperatures from air temperatures for shallow, wind exposed and holomictic water bodies. To evaluate the implications of our results for marine systems, we also analyzed water temperature data of Marsdiep, a tidal inlet to the Waddensea. The lake water temperature model fitted equally well to all four water bodies. Applying the water temperature model to the period 1961–2006 showed an annual increase of 0.042 °C irrespective of lake size and depth. We extrapolated the consequences of lake warming for the onset of growth of larval bream and the size of young-of-the-year bream at the end of the year using an existing fish hatching and growth model. Both models were tested against data from Lake Tjeukemeer, which is intermediate in size compared to Lake Zwemlust and Lake IJsselmeer. The main conclusions of this study are that 1) there is a very tight coupling between air and water temperatures in Dutch shallow lakes, irrespective of their size, resulting in highly similar patterns of lake temperature and a direct translation of climate warming into lake warming; 2) on average water temperature has increased by 2 °C in the period 1961–2006; 3) temperature patterns in the tidal inlet showed a surprising resemblance with the lake temperature patterns, the coastal marine system essentially behaving like an extremely large lake; 4) there are, however, strong seasonal patterns in the extent of warming in a given period of the year; 5) lake warming leads to ca. 3 weeks earlier onset of growth and 20 mm larger sizes in bream during 1971–2006 under the assumption of temperature limited growth in these eutrophic ecosystems.