Protozoan periphytons with their ecological features are considered as a robust bioindicator for bioassessment of both environmental stress and anthropogenic impacts in aquatic ecosystems. In this study, a 1-year baseline survey was conducted using glass slides in coastal waters of Yellow sea, China. Four sampling sites (A–D) were selected from a clean area to a polluted station, and samples were collected monthly at a depth of 1 m. Environmental variables such as salinity, chemical oxygen demand (COD), dissolved oxygen (DO), soluble reactive phosphates (SRP), ammonium nitrogen (NH4-N) and nitrate nitrogen (NO3-N) were measured synchronically to compare with biotic factors. From a total of 144 identified protozoan species, 53 functional units (FUs) were proposed based on four biological traits: feeding type, resource of food supply, body size and movement type. These FUs represented a clear variability in spatial distribution among four study sites. Relative abundances of sessile colonial bacterivores (e.g., BOS5s) showed an increasing trend from sites A to D. Multivariate analysis revealed that the patterns of protozoan FUs showed a significant variation among four sampling sites, and were driven by the increasing levels of nutrients (e.g., NH4-N) and decreasing ranks of DO (P<0.05). The bacterivorous FUs (e.g., BOS5s and BIS3v) were significantly positively related to NH4-N, while the vagile algivorous FUs (e.g., AIS8v, AOS3v, AOS6v) and sessile predators (e.g., RIS4s) were significantly positively correlated with transparency. These findings suggested that FUs of protozoan periphytons may be used as a useful bioindicators of water quality status in marine ecosystems.