Eutrophication, climate change, and river flow fragmentation are the main cause of nuisance algal blooms worldwide. This study evaluated the conditions that trigger the growth and occurrence of nuisance phytoplankton in the Santa Lucía River, a subtropical floodplain lotic system that supplies drinking water to 60% of the population of Uruguay. The main variables that explained phytoplankton biovolume were extracted from generalized linear models (GLM). The potential impact of nuisance organism advection on water utility was estimated by the phytoplankton biovolume transport (BVTR, m3 day-1), an indicator of biomass load. Santa Lucía River had a wide flow range (0.7×105-1438×105 m3 day-1) and eutrophic conditions (median, TP: 0.139 mg L-1; TN: 0.589 mg L-1). GLMs indicated that phytoplankton biomass increased with temperature and soluble reactive phosphorus. Contrary to expectations, the presence of cyanobacteria was positively associated with periods of high flow that result in high cyanobacterial biovolume transport, with a probability of 3.35 times higher when flow increased by one standard deviation. The cyanobacterial biovolume transported (max: 9.5 m3 day-1) suggests that biomass was subsidized by allochthonous inocula. Biovolume from other nuisance groups (diatoms, cryptophytes, and euglenophytes) was positively associated with low-flow conditions and high nutrient concentrations in the main river channel, thereby indicating that these conditions boost eukaryote blooms. The evaluation of BVTR allows a better understanding of the dynamics of fluvial phytoplankton and can help to anticipate scenarios of nuisance species transport.