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Water quality management strategies focus primarily on reducing nutrient loading in estuaries to limit total chlorophyll a (chl a) to less than 40gl(-1). However, potential alterations in phytoplankton community composition and subsequent ecological implications below this limit are not generally considered. The effect of moderate loadings of nitrate (N) and phosphate (P) on nutrient-limited phytoplankton composition and cell size was investigated using multiple bioassays from 2014 to 2016 to evaluate phytoplankton community shifts below the 40gl(-1) threshold. Water collected from North Inlet Estuary, SC, was spiked with 20moll(-1) N and of 10moll(-1) P and incubated for 2days. The proportion of diatoms, cryptophytes, cyanobacteria, prasinophytes, and chlorophytes was calculated for each treatment (i.e., control and NP addition) and for two size fractions (i.e., <20m and whole water). Phytoplankton biomass increases were below the 40g chl al(-1) threshold and resulted in a variable shift in phytoplankton group abundances, likely due to the initial community composition. Nutrient additions enhanced the biomass of the fraction smaller than 20m and the proportion of diatoms at the expense of cyanobacteria and cryptophytes. Shifts in community composition could have potential cascading impacts on higher trophic levels in the estuary. These results highlight the importance of characterizing and monitoring eutrophication using abundances of algal groups in addition to total biomass as ecologically relevant alterations may occur at low levels of eutrophication.