The oceans are changing on a global scale. Zooplankton of the marine ecosystem are microscopic myriads of diverse, floating and drifting animal-like organisms found either on or near the surface of water bodies. Zooplankton samples were collected from the surface water and substratum of the ship hull during the study period from June 2015 to May 2016. Population density ranged from 68 000 to 194 000 cells/L was recorded in the water and substratum of the ship hull. Shannon–Wiener’s diversity index (H') values ranged from 4.97 to 5.57 (bits/ind) at station I and station II. Simpson’s richness ranged from 0.967 and 0.977 at station I and station II. Pielou’s evenness index (J') ranged from 0.976 to 0.994 at station I and station II, respectively. In total, 56 and 48 zooplankton species were recorded in water and substratum of the ship hull in the Chinnamuttom harbor water, respectively. Among the recorded zooplankton, calanoid copepod was found to be dominant followed by ciliata, cyclopoida, harpacticoida, polychaeta, amphipoda and barnacle nauplii in water samples, whereas in substratum samples the Harpacticoid copepod was predominant followed by ciliata, cyclopoida, calanoida, polychaeta, amphipoda and barnacle nauplii. Among the estimated zooplankton, the copepods were found to be dominant throughout the year in the selected site and seasons with appreciable numbers.