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We recently documented that during times of extreme shallow depth, there are severe effects on the water quality of one of the largest shallow lakes in the southeastern USA-Lake Apopka. During those times, total phosphorus (TP), total nitrogen (TN), chlorophyll-a (Chl-a) and toxic cyanobacteria blooms increase, and Secchi transparency (SD) declines. The lake recovers when water levels rise in subsequent years. In this paper, we determined whether extreme shallow depth events, particularly when they re-occur frequently, can stop the long-term recovery of a shallow eutrophic lake undergoing nutrient reduction programs. Apopka is an ideal location for this case study because the State of Florida has spent over 200 million USD in order to reduce the inputs of P to the lake, to build large filter marshes to treat the water, and to remove large quantities of benthivorous fish that contribute to internal P loading. We obtained data from 1985 to 2018, a period that had relatively stable water levels for nearly 15 years, and then three successive periods of extreme shallow depth, and we examined the long-term trends in TP, TN, Chl-a, and SD. There were significant decreasing trends in all of these water quality variables, and even though water quality deteriorated during periods of extreme shallow depth, and reduced the slope of the long-term trends, it did not stop the recovery. However, in the future, if climate change leads to more frequent shallow depth events, which in lakes such as Apopka, result in the concentration of water and nutrients, it is unclear whether the resilience we document here will continue, vs. the lake not responding to further nutrient input reductions.