The composition and dynamics of phytoplankton assemblages during the spring bloom in a shallow, coastal-plain estuary were characterized by high-performance liquid chromatography (HPLC)-derived pigment profiles. From mid-February through the first week in June 1991, samples were collected twice weekly at 2 sites within the Newport River estuary, North Carolina, USA. Pigment profiles, reflecting phytoplankton assemblages dominated by diatoms, dinoflagellates, prymnesiophytes, cryptophytes, and chlorophytes, were compared to phytoplankton cell counts. There were significant ( p 5 0.0005, r 2 = 0.49 to 0 63) relationsh~ps between the taxon-specific pigment concentrations and the taxon-specific cell numbers HPLC-determined chlorophyll (chl) a biomass corresponded wlth the sum of the taxon-spec~fic chl a biomass ( p S 0.001, r2 = 0.95). Each taxon-specific biomass was calculated based on chl a:accessory pigment ratlos determined by regression analyses. Chl a biomass was also measured fluorometr~cally and compared with the HPLC results. Fluorometric analysis underestimated bio~nass when prymnesiophytes, cryptophytes, and chlorophytes dominated the phytoplankton. Despite the inherent environmental vanability of the estuarine sampling location, HPLC-derived pigment profiles did provide division-level phylogenetic assessment of large, short-term changes in the phytoplankton composition and detected assemblage responses to event-scale perturbation effects (e.g. precipitation, wind). These results demonstrate that even in highly variable environments HPLCbased pigment analysis is a valuable tool, providing complementary information to the traditional methodology of cell counting.