Colonization of periphytic ciliates and their usefulness for monitoring water quality were evaluated using the glass slide method in two enclosed mariculture ponds used to culture crab larva and in a natural seawater reservoir. The results revealed that (1) the ciliate species composition and colonizing process differed between the culturing ponds and the natural reservoir and (2) the dominant ciliate species showed a greater distribution in terms of both the abundance and the occurrence frequency. This study also demonstrated that structural parameters were strongly related to water conditions. For example, the abundance was positively associated with NO-3-N and soluble reactive phosphate (P < 0.05), whereas the species number, species diversity and evenness were negatively correlated with nutrients (e.g. NO-3N and NH3-N) and temperature (P < 0.05). These findings support the evidence that periphytic ciliates are useful bioindicators of water quality in enclosed mariculture ecosystems.