For the bioassessment of tropical marine ecosystem, a survey of protozoa colonizing artificial substrate was conducted in the coastal waters of northern Bay of Bengal, Bangladesh. Protozoan samples were collected using glass slides from 1 and 2 m water depths at time intervals of 3, 7, 10, 14, 21, and 28 days during winter and monsoon seasons. Thus, the colonization processes of protozoa were assigned into three stages namely the initial (3 days), transitional (7 days), and equilibrium stages (10–28 days) at two depths in two seasons. Regression analyses demonstrated that the colonization dynamics of protozoa were well fitted to the MacArthur-Wilson model and logistic equation. Species richness reached equilibrium after 10–14 days and species abundance was maximum at a depth of 1 m. These results suggest that samples of protozoa can be collected at 1 m depth in winter season for monitoring the ecological health of tropical marine ecosystems.