Calanid copepods zooplankton play important roles in the marine food web as an intermediate between primary and fish production at higher trophic levels. Their main ecological role is to provide sustenance for fish larvae and adult fish such as whalesharks, manta rays and sardines. This study described the species composition, spatio-temporal distribution and abundance, body sizes and lipid content of calanids, in an upwelling area off Sindangan Bay and in an estuarine plume in Butuan Bay and Gingoog Bay. Five species were identified in two sampling sites: Nannocalanus minor, Undinula vulgaris, Cosmocalanus darwini, Canthocalanus pauper and Neocalanus gracilis. In terms of body sizes, smaller sizes can be seen in the upper shallow strata (0-65 m and 65-135 m) of an upwelling area while larger ones could be seen in the same strata of an estuarine plume. Findings showed that the shallower the water, the more abundant are the calanids associated with an upwelling system and an estuarine plume. The overall results from the correlation analysis revealed that predictors of water physico-chemical parameters such as chlorophyll, salinity and temperature contributed significantly to the abundance and distribution of calanid species but negatively correlated with water depth off Zamboanga del Norte and Agusan del Norte.