In order to evaluate the environmental status within a mariculture pond, temporal variations of physico-chemical factors, protist community structure and interactions between biota and environmental conditions were investigated during a complete cycle in semi-enclosed shrimp-farming waters near Qingdao, north China. Results revealed that: (1) a total of 54 protist taxa with ten dominant species was present, comprising 4 chlorophyceans, 2 chrysophyceans, 5 cryptophyceans, 10 dinoflagellates, 3 euglenophyceans, 10 diatoms, 18 ciliates and 2 sarcodines; (2) a single peak of protist abundance occurred in October, mainly due to the chlorophyceans, diatoms and chrysophyceans, while the bimodal peaks of biomass in July and October were mainly due to the ciliates, dinoflagellates and diatoms; (3) the succession of protist communities significantly correlated with the changes of nutrients, salinity and temperature, especially phosphate, either alone or in combination with NO3; (4) species diversity and evenness indices were found to be relatively independent of physico-chemical factors, whereas species richness and the ratio of biomass to abundance were strongly correlated with water temperature and abundances of bacteria. It was concluded that planktonic protists are potentially useful bioindicators of water quality in a semi-enclosed mariculture system.