There was a unique brackish water ecosystem and affected a change in the plankton composition at lagoon and riverside in Segara Anakan Cilacap. The research purpose was to map phytoplankton and zooplankton composition consisting of freshwater and sea water plankton from lagoon to sea water entrance in the west part of Segara Anakan Cilacap. Survey method was taken with purposive random sampling in fourteen stations and four replicates with new and full moon conditions from March to April 2018 in a wet season. The result showed 52 species of plankton. All species belonged to phylum Cyanophyta (9 species), Chlorophyta (13 species), Chrysophyta (19 species), Euglenozoa (2 species), Rotifera (2 species) and Arthropoda (7 species). Of the 52 species collected in all stations and replicates, phytoplankton has a greater species richness (41 species) than zooplankton (11 species). And also, freshwater plankton (47 species) has a greater species richness than sea water plankton (5 species). The wet season caused freshwater enters brackish water. The largest freshwater of River Citanduy enters the brackishwaters of Segara Anakan Cilacap and causing the dominan species of phytoplankton and freshwater plankton in this area of inland waters.

plankton composition; brackish water; Cilacap