The colonization features of periphytic protozoa have proved to be a useful tool for indicating water quality status in aquatic ecosystems. In order to reveal the seasonal variations in colonization dynamics of the protozoa, a 1-year baseline survey was carried out in coastal waters of the Yellow Sea, northern China. Using glass slides as artificial substrates, a total of 240 slides were collected at a depth of 1 m in four seasons after colonization periods of 3, 7, 10, 14, 21, and 28 days. A total of 122 ciliate species were identified with 21 dominant species. The colonization dynamics of the protozoa were well fitted to the MacArthur-Wilson and logistic models in all four seasons (P < 0.05). However, the equilibrium species numbers (S_eq), colonization rates (G), and the time to 90% S_eq (T_90%) represented a clear seasonal variability: (1) more or less similar levels in spring and autumn (S_eq = 29/23; G = 0.301/0.296; T_90%=7.650/7.779); (2) with a significant difference in summer and winter (S_eq = 32/121; G = 0.708/0.005; T_90% = 3.252/479.705). Multivariate approaches demonstrated that the exposure time for the species composition and community structure of the protozoa to an equilibrium period were 10–14 days in spring and autumn, but less and more time periods were needed in summer and winter, respectively. Based on the results, we suggest that the colonization dynamics of periphytic protozoa were different within four seasons, and an optimal sampling strategy for monitoring surveys should be modified during different seasons in marine ecosystems.