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Ceratium furcoides (Dinophyta) have gained international attention as invasive aquatic species, especially in South America, due to its fast proliferation into various aquatic systems and the subsequent adverse impacts on water quality and native biota. The present study reports the detection of dense populations of C. furcoides in the Paracambi Small Hydropower Plant (SHP) located in the Guandu River basin. Sampling was conducted at five sites during two sampling events in 2019 and 2020 during different seasons (spring and summer), respectively. We used two different standardized sampling methods, including surface collections (SS) (100‐ml) traditionally used for quantitative analysis of inland water phytoplankton, as well as filtration of 20‐L sub‐surface water (FS) through a zooplankton net. The cell densities were higher in SS (599 individuals/ml) than in FS (0.068 individuals/ml), possibly indicating a patchy distribution of Ceratium in the surface water layers. The total cell length exhibited high values (mean length of 249‐μm; mean width of 67‐μm), possibly accounting for water treatment impairment, an inability of zooplankton to consume them and/or fish gill clogging. This new observation within an extensively investigated area, and a source of water for nine million people, in the present study advocates for integrated samplings that also consider a search for cysts accumulated in the bottom sediments, as well as more detailed spatial and temporal investigations considering the salient features of C. furcoides' populations. [ABSTRACT FROM AUTHOR]