The study characterized the spatiotemporal variations in composition, abundance, and diversity of zooplankton community in Manila Bay. Zooplankton samples were collected every two months within three years from 2013 to 2015. The zooplankton composition of Manila Bay includes 29, 52, and 50 taxa in 2013, 2014, and 2015, respectively belonging to the following major groups: Copepoda, Decapoda, Cladocera, Chordata, Annelida, Mollusca, Chaetognatha, Ciliophora, Foraminifera, Echinodermata, and Chromista. Copepod nauplii consistently dominated the zooplankton community in the bay from 2013 to 2015 followed by Tintinnids, Oithona spp., Euterpina acutifrons, and Paracalanus spp. The highest concentration of zooplankton was specifically observed in the southwestern side near the mouth of the bay (Station 4) in July 2015. In 2014, the highest recorded zooplankton density was in the month of November in the eastern side (Station 10). In general, relatively high diversities of zooplankton community were recorded in many months in 2015 as compared to 2013 and 2014 although the highest recorded diversity occurred in March 2014. Redundancy Analysis revealed salinity, temperature, dissolved oxygen, chlorophyll a, PO4, SiO, and NO3 to have a strong correlation with the zooplankton abundances and distribution.