Colonization features of biofilm-dwelling protozoa, especially ciliates, are routinely used as a useful tool for marine bioassessment. In this review, we summarize some of these features to develop an optimal sampling strategy for using biofilm-dwelling protozoa as bioindicators of marine water quality. We focus on the utility of: (1) diversity indices to analyze the colonization features of biofilm-dwelling protozoa for monitoring marine water quality; (2) MacArthur–Wilson and logistic equation models to determine spatio-temporal variations in colonization dynamics; and (3) homogeneity in taxonomic breadth of biofilm-dwelling protozoa during the process of colonization. The main findings are that: (1) the colonization dynamics of biofilm-dwelling protozoa are similar at depths of 1–5 m in spring and autumn; (2) temporal variability was well fitted to the MacArthur–Wilson and logistic models ( P < 0.05); and (3) species composition reached an equilibrium after a colonization period of 10–14 days in spring and autumn, but this took less time in the summer and more time in the winter. Ellipse-plotting tests demonstrated spatial variability in homogeneity in taxonomic structure of the ciliate communities at different depths in the water column, with high levels at 1 m and 2 m and lower levels at 3.5 m and 5 m. Thus, the findings of this review suggest that the colonization dynamics of biofilm-dwelling protozoa may be influenced by different depths and seasons in coastal waters and 1–2 m in spring and autumn may be optimal sampling strategy for bioassessment on large spatial/temporal scales in marine ecosystems.