Protistan communities are characterized by high ecological and species diversity due to their short life cycles and by a quick response to environmental changes. Many species respond rapidly to pollutants and often inhabit environments that are unfavorable to most of metazoans and some can even tolerate extremes of environmental conditions to macrofauna. As predominant components of protistan communities, ciliates and flagellates may react more quickly to environmental changes than any other eukaryotic organisms because of their rapid growth and delicate external membranes and can thus serve as bioindicators of water pollution. Polyurethane foam unit (PFU) is an artificial substrate able to host planktonic, periphytic and benthic protistan assemblages. The PFU method has been widely and successfully employed to evaluate freshwater quality all over the world. However, as far as we know, this method has not been used in marine habitats as effective as in freshwater biotopes because of the influence of tidal current and circulation in near-shore area. In order to evaluate the feasibility of using the PFU method to assess coastal water quality, Xu et al.modified the conventional PFU method and presented a bottled PFU (BPFU) system and successfully used to evaluate the water quality in Korean coastal waters. Our study is the first to use the BPFU method for bioassessment in Chinese offshore areas. Three stations in the coastal waters off Qingdao, China were selected as study area from September to October in 2007. Margalef diversity index was calculated by d= (S-1)/lnN. The relationship between the protistan community parameters and marine water quality was analyzed. MacArthur and Wilson equilibrium model: S_t=S_eq (1-e^-Gt) was applied to assess the colonizing process of protistan communities. A total of 263 species of protists were identified during the survey. Among these were 83 diatoms, 59 flagellates, 31 sarcodines, and 90 ciliates. In terms of species composition, site 1 was dominated mainly by bacterivores (e.g., Euplotes parabalteatus, Uronema marinum and Pleuronema coronatum), site 3 mainly by algivores (e.g., Strombidinopsis minima, Strombidium apolatum and Hartmannula augustipilosa), and site 2 was in an intermediate status. These results are consistent with the environmental conditions: site 3 had the best water quality, site 1 was the most eutrophic site, and site 2 was the moderate one. Furthermore, the colonization processes and functional parameters (i.e. S_eq, G and T_90%) of communities correlated with the pollution status and could thus clearly discriminate the different classes of water quality as measured by physicochemical indicators. But the Margalef diversity index did not coincide with the water conditions: site 1 had the highest index value (on average 4.16), while site 2 had the lowest (on average 3.00). Nonetheless, this work further suggests the practicability of the BPFU method for biomonitoring of coastal water pollution. Our study also indicates that protistan communities are more effective and accurate than protozoan communities in reflecting water quality.