In 2011, the Indian River Lagoon, a biodiverse estuary in eastern Florida (USA), experienced an intense microalgal bloom with disastrous ecological consequences. The bloom included a mix of microalgae with unresolved taxonomy and lasted for 7 months with a maximum concentration of 130 μg chlorophyll a L −1 . In 2012, brown tide Aureoumbra lagunensis also bloomed in portions of this estuary, with reoccurrences in 2016 and 2018. To identify and understand the role of grazer pressure (top-down control) on bloom formation, we coupled DNA sequencing with bivalve feeding assays using three microalgae isolated from the 2011 bloom and maintained in culture. Feeding experiments were conducted on widely distributed bivalve species in the lagoon, including eastern oysters ( Crassostrea virginica ), hooked mussels ( Ischadium recurvum ), charru mussels ( Mytella charruana ), green mussels ( Perna viridis ), Atlantic rangia ( Rangia cuneata ), and hard clams ( Mercenaria mercenaria ), which were exposed to 3 × 10 4 cells mL −1 of five species of microalgae consisting of A. lagunensis and the three species clarified herein, the picocyanobacteria Crocosphaera sp. and ' Synechococcus ' sp., and the picochlorophyte Picochlorum sp., as well as Nannochloropsis oculata used as a control. To ensure clearance rates were indicative of consumption and assimilation, the microalgae were isotopically ( 15 N) labeled prior to feeding experiments. Clearance rates differed among bivalve and microalgal species, but enriched 15 N values in bivalve tissue suggest that algal bloom species were assimilated by the bivalves. These results expand our understanding of the important ecosystem services that healthy, biodiverse filter feeder communities provide.