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An increase in the distribution and frequency of cyanobacterial blooms has been reported for many regions worldwide. Due to this fact, we studied the variables that influence the abundance of natural populations of planktonic cyanobacteria in temperate lakes of central and southern Chile. These lakes differed in trophic state and watershed use. Cyanobacteria dominated in meso- and eutrophic systems and their occurrence correlated to watershed use (tree plantations and urban). Ochrophyta and Bacillariophyta were dominant in oligotrophic lakes, where native forest dominated land usage. In these lakes, the maximum depth of the euphotic zone influenced the community structure and the genera of cyanobacteria. Dolichospermum was the most abundant, frequent, and widely distributed genus, found in oligotrophic and eutrophic lakes, forming blooms in eutrophic systems.

The concentration of total phosphorus and total nitrogen positively influenced cyanobacterial abundance and bloom formation, mainly by Aphanizomenon, Aphanocapsa, Aphanothece, and Dolichospermum, and Microcystis.

In contrast to many reports on their occurrence in the northern hemisphere, these genera occurred widely at less than 20 degrees C, forming dispersive blooms, at low temperatures in autumn and winter (10.8-15.6 degrees C). This shows that eutrophication is the main factor for bloom formation and these genera can form blooms independent of temperature. However, some genera, such as Microcystis, increased their abundance and presented more intense blooms (scums) at high temperatures. Our study provides baseline data to document long-term changes in lentic systems of the western south-central area of South America, including genera that could respond by increasing their abundance with eutrophication and projected climatic changes.