Climate change has an indirect effect on water quality in freshwater ecosystems, but it is difficult to assess the contribution of climate change to the complex system. This study explored to what extent climatic indicators (air temperature, wind speed, and rainfall) influence nutrients and oxygen levels in a shallow reservoir, Yuqiao Reservoir, China. The study comprises three parts—describing the temporal trends of climatic indicators and water quality parameters during the period 1992–2011, analyzing the potential impacts of climate on water quality, and finally developing a quantitative assessment to evaluate how climatic factors govern nutrient levels in the reservoir. Our analyses showed that the reservoir experienced substantial cold periods (1992–2001) followed by a warm period (2002–2011). The results showed that increasing air temperature in spring, autumn, and winter and increasing annual wind speed decrease total phosphorus (TP) concentration in the reservoir in spring, summer, and winter. According to the quantitative assessment, the increase in air temperature in spring and winter had a larger contribution to the decrease in TP concentration (47.2 and 64.1%), compared with the influence from decreased wind speed and rainfall. The field data suggest that nutrients decline due to enhanced uptake by macrophytes in years when spring was warmer and the macrophytes started to grow earlier in the season. The increasing wind speed and air temperature in spring also significantly contribute to the increase in dissolved oxygen concentration. This study helps managers to foresee how potential future climate change might influence water quality in similar lake ecosystems.