Nhlabane coastal lake and estuary system in South Africa is divided by a permanent barrage constructed at the outlet of the lake. This study compared the zooplankton assemblages of the lake and estuary systems after 15 years of separation. Before sampling commenced the mouth of the estuary closed and remained so throughout the duration of the study. The lake was completely fresh and the estuary had a low salinity not exceeding 4‰. Both the estuary and lake are shallow systems (less than 2 m) and were well mixed. Turbidity levels were generally below 10 NTUs. Temperature fluctuated seasonally between 18.5 and 30°C. Oxygen levels ranged between 4.3 and 9.9 mg/l but were mostly above 5 mg/l for both systems. The estuarine and lake plankton was dominated by copepod instars, especially of the calanoid Pseudodiaptomus hessei. During the entire study period the lake also supported high densities of rotifers. Rotifers only appeared in the estuarine plankton at the end of the sampling period. During the first sampling sessions zooplankton diversity in the estuary was higher but declined thereafter to levels within the range calculated for the lake. Estuarine relict species recorded reflect the estuarine history of the lake. Multivariate analyses indicated a change in the composition of the zooplankton community in the estuary during the duration of the study, while that of the lake remained comparatively stable. Species composition analyses showed that this change in the estuary was due to a shift from an estuarine to a more freshwater zooplankton assemblage. During this change some estuarine species declined in abundance or were not recorded anymore. These changes in the zooplankton community of the estuary may well illustrate the changes that occurred in the lower (south) section of the lake after completion of the barrage which isolated it from the estuary.