Simple, rapid and reliable methods are required to monitor the microbial community change in aquatic pond for better animal performance. Four floc (suspended organic matter) samples were collected from outdoor raceways and tanks used for culturing Pacific white shrimp Litopenaeus vannamei. Twenty-two chlorophyll (Chl) and carotenoid pigments were separated, identified and quantified using high-performance liquid chromatography–ultraviolet/Vis-mass spectrometry in the freeze-dried floc samples. Algal community composition (diatoms, chlorophytes, cyanobacteria, dinoflagellates and cryptophytes) was determined by measuring concentrations of the respective taxonomic biomarkers (carotenoid fucoxanthin, lutein, zeaxanthin, peridinin and alloxanthin) as independent variables and Chl a as the dependent variable using a multiple regression model. This analysis found that the phytoplankton community of the floc samples from two groups of shrimp tanks (32 g L−1-salinity) were diatom-dominated (81.7% and 84.4%); and two floc samples from shrimp raceways (5 and 18 g L−1-salinity) were chlorophyte-dominated (75.4% and 82.3%). Assessment of total algal and bacterial biomass by quantification of Chl a and muramic acid, respectively, indicated that the 18 g L−1-salinity raceway sample was bacteria-dominated, whereas the other three floc samples were algae-dominated. Sample protein quality was evaluated by its essential amino acid (AA) score and index. Arginine and lysine were found to be the two most limiting AAs for all floc samples.