Clear Lake is a large, natural lake in northern California, USA, with many beneficial uses but also substantive environmental issues. The lake has a long history of water quality problems including mercury contamination, pesticide usage, invasive species, and high rates of primary production. In recent years, an increase in cyanobacterial harmful algal blooms (cyanoHABs) has been documented in the lake, adding to the environmental issues faced by aquatic species present in the lake and the local community. Extensive observations of various physical, chemical, and biological parameters in Clear Lake began in the mid-1900s. The most pertinent of these data sets and findings have been reviewed and analyzed with the intent of improving our understanding of the causes and drivers of cyanoHABs, toxin production, and identifying data gaps. Several parameters including average annual water temperature have remained relatively constant over the past 70 years, although the seasonally averaged water temperatures have shifted in a manner that may now favor cyanobacterial dominance. Clear Lake has also witnessed recent changes in several environmental variables such as total phosphorus concentrations that might contribute to blooms. An analysis of lake conditions prior to and following the enactment of a total maximum daily load (TMDL) for phosphorus in 2007 indicates little measurable influence on total phosphorus concentrations in Clear Lake. The present trajectory of lake chemistry suggests that additional research and management efforts will be needed to address the recurrence of cyanoHABs in the future. Future lake management strategies should include consideration of the role of internal nutrient loads to lessen cyanoHABs. Furthermore, a better understanding of cyanobacterial community interactions and top-down effects on bloom formation within the lake can help guide future cyanoHAB management strategies.