The formation of algal and cyanobacterial blooms caused by the eutrophication of water bodies is a growing global concern. To examine the impact of extreme weather events on blooms, eutrophication-related parameters (e.g., water temperature, nitrate, ammonium, nitrite, and soluble reactive phosphate (SRP)) were quantitatively assessed monthly over three years (2017–2019) at Lake Seeburg (Central Germany), a shallow eutrophic lake with regular cyanobacterial blooms. In addition, SRP concentrations in sediment pore water were assessed monthly for one year (2018). The monitoring period included a three-day extremely heavy rain event in 2017 as well as a severe drought in summer 2018. No such extreme weather conditions occurred in 2019. After the heavy rain event in 2017, anoxic water containing high levels of ammonium and SRP entered the lake from flooded upstream wetlands. This external nutrient spike resulted in a heavy but short (3 weeks) and monospecific cyanobacterial bloom. A different situation occurred during the exceptionally hot and dry summer of 2018. Especially favored by high water temperatures, SRP concentrations in sediment pore waters gradually increased to extreme levels (34.4 mg/L). This resulted in a strong and sustained internal SRP delivery into the water column (69 mg/m2·d−1), which supported the longest-lasting cyanobacterial bloom (3 months) within the three-year monitoring period. Subsequent biomass decay led to oxygen-depleted conditions in the bottom waters, elevated ammonium, and, later, nitrate concentrations. Our observations demonstrate the particular effects of extreme weather events on nutrient dynamics and the phytoplankton composition in the lake. As the frequency and intensity of such events will likely increase due to climate change, their impacts need to be increasingly considered, e.g., in future remediation strategies.