Intensive growth of aquatic macrophytes interferes with water quality and ecosystem dynamics worldwide. Although mechanically removing macrophytes is the most commonly used method for their eradication, it can also cause undesirable disturbances in aquatic reservoir communities. We performed laboratory incubations of phytoplankton sampled before and after macrophytes were mechanically removed from the Piraquara II reservoir, South Brazil. We analyzed changes in growth and composition of the main phytoplankton groups with respect to nutrient shifting. Prior to removing the macrophytes, the phytoplankton community was dominated by low cell abundances of diatoms and flagellates. In contrast, growth rates of cyanobacteria (mainly Cylindrospermopsis raciborskii, Pseudanabaena sp., and Geitlerinema sp.) and of colonial chlorophytes were favored after macrophyte removal, while the abundances of diatoms and flagellates decreased. Our results suggest that removing macrophytes causes dramatic changes in phytoplankton composition and biomass and selects for toxigenic species of cyanobacteria. These changes were probably associated with the disturbance caused by removing the macrophytes, which immediately created new environmental conditions prone to species competition. These findings indicate that the use of mechanical techniques to manage macrophytes should be carefully considered, along with monitoring of harmful species and changes of limnological parameters.

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