Biofilm-dwelling protozoa are a primary component of microbiota and play important roles in the functioning of microbial food webs such as the mediation of carbon and energy flux from plankton to benthos in marine ecosystems. To demonstrate the vertical pattern of the protozoan communities, a 1-month baseline survey was carried out in coastal waters of the Yellow Sea, northern China. A total of 40 samples were collected using glass slides as artificial substrates at four depths: 1, 2, 3.5 and 5 m. A total of 50 species were identified, comprising seven dominant and eight commonly distributed species. Species richness and individual species abundances showed a clear decreasing trend down the water column from 1 to 5 m, although the former peaked at a depth of 2 m. Multivariate approaches revealed that protozoan community structure differed significantly among the four depths, except for those at 2 and 3.5 m. Maximum values of species richness, diversity and evenness generally decreased with depth although they peaked at either 2 or 3.5 m. These results suggest that water depth may significantly shape the community patterns of biofilm-dwelling protozoa in marine ecosystems.