The increasing occurrence of cyanobacterial bloom in freshwaters worldwide is of great importance because of public health risks. In addition, they are very likely to have negative impact on ecological and economic aspects. In this study, the seasonal succession of phytoplankton population in Lake Karaoun in Lebanon was monitored from May 2009 to June 2011. The physicochemical parameters of lake water were then monitored for 1 year, from June 2010 until June 2011, to correlate the physicochemical parameters with the phytoplankton population in the lake. Our results showed, for the first time in Lebanon, that the eutrophied Lake Karaoun has been under the invasion of toxic cyanobacterial blooms since May 2009. The cyanobacterial bloom was persistent from late spring (May) until late fall (December) for 2 consecutive years. The high water temperature in the summer season is the main factor that has been affecting the growth of the cyanobacteria. The most frequently encountered bloom-forming species were Microcystis aeruginosa and Aphanizomenon ovalisporum, which were either present individually or coexistent. The obtained results showed that during the period of cyanobacterial bloom, a deterioration of water quality defined by low levels of dissolved oxygen, total dissolved solids, and electric conductivity was reported. During cyanobacterial bloom period, the concentration of the orthophosphate–P (PO4-P) was very minimal. The measured high value of chlorophyll-a concentration during cyanobacterial bloom period (48.6 μg/L) was attributed to high photosynthetic activity. Cyanobacterial blooms can cause a variety of water-quality problems in Lake Karaoun in addition to human health risk.