Fish kills are a recurring phenomenon in hypereutrophic lakes. The effects of a sudden injection of anoxic bottom water into surface waters are well known, as well as the degradation of phytoplankton blooms and the release of phytoplankton toxins. However, in this study we report on a new, climate-related cause of fish kills in a shallow lake. We observed that a long period of drought in a hot summer followed by heavy rain resulted in a large input of labile organic matter. This was followed by a condition of whole-lake anoxia and fish kill in the lake basin receiving the input, while the second basin, immediately downstream, was left unaffected. To test the causal relationship between these events, an oxygen model calculated that respiration had increased by 230% following the organic input and caused whole-lake nocturnal anoxia for four days despite unaltered daytime photosynthesis. One year after the fish kill, roach and bream had migrated from the downstream lake basin and re-established dense populations, while large predatory perch and pike remained very few. This imbalance in the fish food webs may last for several years and in turn increase predation on zooplankton and release phytoplankton from grazing control. The prolonged effects of fish kills on fish and lake community structure demand further research, as weather-induced anoxia can be expected to become more common.