Water quality degradation is one of the largest threats to freshwater ecosystems. Nutrient inputs, land use changes, and climate are expected to be the most important drivers of water quality degradation. Here, we quantify the relative influence of nutrient inputs, climate, and lake geomorphometry on primary production in freshwater lakes globally, using chlorophyll a (chla) as a proxy. We used a large lake chlorophyll database that included chla and total phosphorus, in addition to lake geomorphometric variables (mean depth, watershed area, elevation, surface area, volume, residence time) and climate (air temperature, precipitation, cloud cover, solar radiation) for 2561 freshwater lakes around the globe. Our model was able to explain 60% of the variation in chla concentrations. Of that, total phosphorus (TP) explained 42%, a combination of climate variables explained 38%, and geomorphometrics explained 20% of the variation. Although there have been increased efforts and regulations in place for land use and farming, nutrient inputs continue to be the leading cause of primary production in lakes. However, the influence of climatic variables acting synergistically (temperature, precipitation, cloud cover and solar radiation) is nearly equal to that of total phosphorus, suggesting nutrient management efforts are not sufficient alone to mitigate water quality degradation. Our findings underscore the critical need to incorporate climate factors into water quality management given current climate change.