The occurrence of cyanobacterial blooms has increased globally over the last decades, with the combined effect of climate change and eutrophication as its main drivers. The seasonal dynamic of cyanobacterial blooms is a well-known phenomenon in lakes and reservoirs in temperate zones. Nevertheless, in the tropics, most studies have been performed in shallow and artificial lakes; therefore, the seasonal dynamic of cyanobacterial blooms in deep and eutrophic tropical lakes is still under research. We studied the seasonal variation of the phytoplankton community and the factors associated with Microcystis aeruginosa blooms along the water column of Lake Alberca de Tacámbaro, a warm monomictic crater lake located in Mexico, during 2018 and 2019. According to previous studies performed in 2006 and 2010, this lake was mesotrophic-eutrophic, with Chlorophyta and Bacillariophyta as the dominant groups of the phytoplankton community. During 2018 and 2019, the lake was eutrophic and occasionally, hypertrophic, a phenomenon likely associated with the increase of farmland area around the lake. The dominant species was M. aeruginosa, forming blooms from the surface to 10 m depth in winter, in the hypolimnion in spring and summer, and along the full water column in autumn. These findings suggest that M. aeruginosa in Lake Alberca de Tacámbaro displays seasonal and spatial population dynamics. Total phosphorus, dissolved inorganic nitrogen, water temperature and photosynthetically active radiation were the environmental factors related to M. aeruginosa blooms. Our results suggest that the changes in the structure of the phytoplankton community through time, and M. aeruginosa blooms in Lake Alberca de Tacámbaro, are mainly related to changes in land use from forest to farmland in areas adjacent to the lake, which promoted its eutrophication in the last years through runoffs. Comparative studies with other deep and eutrophic lakes will allow us to gain a deeper understanding of the dynamic of cyanobacterial blooms in natural and artificial water reservoirs strongly stressed by human activities.