Eutrophication has been identified as the primary cause of water quality deterioration in inland waters worldwide, often associated with algal blooms or fish kills. Eutrophication can be controlled through watershed management and in-lake measures. An extreme heatwave event, through its impact on mineralization rates and internal nutrient loading (phosphorus—P, and nitrogen—N), could counteract eutrophication control measures. We investigated how the effectiveness of a nutrient abatement technique is impacted by an extreme heatwave, and to what extent biogeochemical processes are modulated by exposure to heatwaves. To this end, we carried out a sediment-incubation experiment, testing the effectiveness of lanthanum-modified bentonite (LMB) in reducing nutrients and greenhouse gas emissions from eutrophic sediments, with and without exposure to an extreme heatwave. Our results indicate that the effectiveness of LMB may be compromised upon exposure to an extreme heatwave event. This was evidenced by an increase in concentration of 0.08 ± 0.03 mg P/L with an overlying water volume of 863 ± 21 mL, equalling an 11% increase, with effects lasting to the end of the experiment. LMB application generally showed no effect on nitrogen species, while the heatwave stimulated nitrification, resulting in ammonium loss and accumulation of dissolved oxidized nitrogen species as well as increased dissolved nitrous oxide concentrations. In addition, carbon dioxide (CO2)-equivalent was more than doubled during the heatwave relative to the reference temperature, and LMB application had no effect on mitigating them. Our sediment incubation experiment indicates that the rates of biogeochemical processes can be significantly accelerated upon heatwave exposure, resulting in a change in fluxes of nutrient and greenhouse gas between sediment and water. The current efforts in eutrophication control will face more challenges under future climate scenarios with more frequent and intense extreme events as predicted by the IPCC.