The results of two surveys during the rainy season (11/2008) and dry season (4/2009) identified 124 species of zooplankton, in which copepoda were most diverse with 68 species (55 percent), followed by cladocera (15 percent). The total number of species in the lagoon (111 spp) was 3.4 times compared to that in the rivers (33 spp). The density of zooplankton was relatively high with an average of 19358.5 inds/m3. The average density of zooplankton in the lagoon (23,656 inds/m3) was 22 times compared to that (1,091 inds/m3) in the rivers. Copepoda was abundant, with an average density of 17,820 inds/m3, . corresponding to 92.1 percent of the total zooplankton. The average density of zooplankton in the dry season (34,459 inds/m3) was 8 times (4,257 inds/m) compared to that in the rainy season. On the basis of the Bray-Curtis similarity index, there were two distinct groups those in the lagoon and in the rivers. In the rivers the species evenness (Pielou J') and the diversity index (Shannon H') were both significantly higher than those in the lagoon while the species richness (Margalef's d) in the lagoon (4.3) was 2 times compared to that in the rivers (2.4).