This report covers high performance liquid chromatography (HPLC) derived pigment based chemotaxonomy for phytoplankton studies in a turbid coastal environment. Sediment resuspension brings detritus with pheopigments and other chlorophyll (CHL) breakdown products into the water column and hampers data interpretation. Two hundred sixty six water samples from Florida Bay were analyzed from monthly collections (Sept. 2000-Aug. 2002. Comparing biomarker estimated CHLa to measured CHLa, we found a mean of 105.4% (Std. Dev. ¼ 24.7; R 2 ¼ 0.9547) and when data was restricted to those samples with ,10% pheopigments, estimations improved to 102 + 16%. It is concluded that all HPLC studies on phytoplankton communities must report the percentage pheopigments.