A new approach is chosen to visualize ecosystem health by using parasite bioindicators in Segara Anakan Lagoon, a brackish water ecosystem at the southern Java coast, Indonesia. Three fish species (Mugil cephalus, Scatophagus argus, Epinephelus coioides) were collected in two different years and sampling sites and studied for ecto- and endoparasites. Additional data were taken for E. coioides from two further sites in Lampung Bay, Sumatra, and for E. fucoguttatus out of floating cages from a mariculture facility in the Thousand Islands, Jakarta Bay, North Java. The parasite fauna of fishes inside the lagoon was characterized by a high number of ecto- and a low number of endoparasites, the endoparasite diversity was relatively low and the prevalence of ectocommensalistic trichodinid ciliates was high. These parameters were chosen to indicate the biological conditions inside the lagoon. In E. coioides during rainy season, the prevalence of trichodinid ciliates was highest inside the lagoon (55%) compared with 27% in an open-net-cage mariculture and 5.7% in free-living specimens in Lampung Bay. The endoparasite diversity (Shannon-Wiener) was lowest in fish from Segara Anakan lagoon (0.66) compared with fish from an open-net-cage mariculture (0.71) and free-living specimens (1.39). Results for E. fuscoguttatus from the mariculture site in the Thousand Islands, a relatively undisturbed marine environment, demonstrated high parasite diversity (1.58) in the cultivated fish, a high number of endoparasites, and no trichodinids. A star graph is used to visualize the parasite composition for the different fishes, sampling sites, and conditions, using (1) the prevalence of trichodinid ciliates, (2) the ecto/endoparasite ratio and (3) the endoparasite diversity as bioindicators. The application of the star graph is suggested to be a suitable tool to visualize and monitor environmental health under high parasite biodiversity conditions within tropical ecosystems. It can also support a better communication to stake holders and decision makers in order to monitor environmental impact and change.