The present investigation used Brachionus plicatilis (Rotifera) to evaluate the water quality in Callao Bay, Peru. The water samples were taken in four areas: P1 in La Punta, P2 in Chucuito, P3 in front of the Callao Port Terminal and P4 in the San Lorenzo and El Frontón Islands, and in four seasonal periods: autumn-2015, winter- 2015, spring-2015, and summer-2016. Physical-chemical parameters, chlorophyll, phycocyanin, heavy metals, and bioassays with seawater at 24 h and 48 h of exposure to Brachionus plicatilis obtained from a standardized culture were evaluated in each area and seasonal period. High concentrations of Ag, Pb, Hg, Cu, Cr, Ni and Zn were found at all the sampling sites. The no observed effect concentration (NOEC) values (concentration at which a significant effect of mortality is not observed with respect to the control) and lowest observed effect concentration (LOEC) (minimum concentration at which a significant effect of mortality is observed with respect to the control) at 48 h of exposure to the B. plicatilis bioassay were lower for P1 (winter-2015) and P2 (winter-2015). Principal components analysis (PCA) showed that principal component 1 (PC1) contributed 38.70% and PC2 17.70%. PC1 was formed by LOEC of Cd, Hg, Ni, Ag, and Pb while PC2 was related to Cu, Cr and Zn. According to these results Brachionus plicatilis can be used as a bioindicator organism to assess water quality in the marine environment.