Water level fluctuations (WLFs) affect phytoplankton dynamics, water quality, and fish populations in lakes and reservoirs around the world. However, such effects are system-specific and vary due to interactions with other external factors such as solar radiation, air temperature, wind, and external phosphorus loading. Utilizing data from a long-term monitoring program (1990–2016), we developed an approach using cross-tabulation contour and conditional probability analyses to detect the effects of WLFs on the frequency of poor water quality impacting native fish in a large, shallow, hypereutrophic lake. Through the incorporation of long-term inter-annual and seasonal variability in climatic factors and cyanobacterial bloom periodicity, our approach detected non-linear WLF effects whereby both high and low-lake levels were associated with higher probabilities of poor water quality conditions stressful to fish including high pH, high un-ionized ammonia, and low dissolved oxygen. Although lake level management may not prevent poor water quality in any given year due to other external factors such as temperature or wind, we determined that seasonally based intermediate lake levels bracketing the long-term median afforded the best water quality conditions for endangered fish during the summer period when poor water quality is most common.
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