Stratification is well developed in Msikaba estuary and has a major influence on the distribution of the zooplankton. The oligohaline zooplankton component does not become well established, while marine zooplankton organisms penetrate relatively far up the estuary in the high salinity bottom waters. The euryhaline component becomes relatively well established near the mouth and it would appear that these organisms maintain their position within the estuary by vertical migration between inflowing bottom and outflowing surface waters. Seasonal means of zooplankton biomass were similar and ranged between 16 mg/m8 of water during winter and 15 mg/m8 during summer.