We analyzed the phytoplankton interactions during a Ceratium furcoides invasion along with the environmental variables contributing to its dominance and blooms in Marrecas, a south-Brazilian reservoir. We monitored Marrecas weekly/monthly (n = 116) from 2014 to 2018. C. furcoides avoided summer and preferred spring, which displayed optimal temperatures for the species (15–23 °C), exhibiting in October 2014 the maximum density ever reported (15,865 ind. mL-1). It showed direct correlation with iron, manganese, and turbidity; evidencing dependency of a mixing regime which triggers cyst resuspension (interrupting cysts’ dormancy). Cryptomonas spp., Komma caudata, Discostella stelligera and after 2016 also Chlamydomonas sp. were the only species present during C. furcoides blooms. Komma caudata, Cryptomonas sp., and Aulacoseira alpigena correlated positively with the invader, as all prefer turbulent waters. C. furcoides correlated negatively with Chlorophyta (mainly Chlamydomonas spp.) which is vulnerable to mixing, and Bacillariophyta (Urosolenia eriensis and Discostella stelligera) that prefers clear waters. It also showed a consistent negative correlation with Ochrophyta (Mallomonas spp.), Cyanobacteria (Microcystis), and Urosolenia eriensis; suggesting competition for resources. Furthermore, it correlated negatively with species richness. Notwithstanding, based on the decrease of blooms, the phytoplankton community appears to have reached a more stable state (homogeneous species representation). However, further monitoring is required for confirmation.