Biofilm-dwelling ciliates are a primary component of a biofilm, and play an important role in the functioning of microbial food webs by mediating carbon and energy flux into benthos from plankton. The carbon flux of biofilm-dwelling ciliates was studied at different trophic-functional levels within the colonization process in coastal waters of the Yellow Sea, northern China from May to June 2015. Samples were collected, using a glass slide method, at the time intervals of 1, 3, 7, 10, 14, 21 and 28 days from depths of 1 and 3 m. The carbon biomass of both total ciliates and all trophic-functional groups increased following the logistic growth curve model. During the whole colonization period, the bacterivores and non-selectives were generally the primary contributor to the carbon flux in young samples (<14 days), while the algivores and raptors predominated mature samples (14–28 days) at both depths. In terms of mature samples, however, the non-selectives and algivores were the primary contributors at a depth of 1 m, while the raptors accounted for primary contributions to the carbon flux at a depth of 3 m. Although the times to 50% maximum carbon biomasses were generally ranged 24 days at both depths, the maximum carbon biomasses were significantly higher at depth of 3 m than at 1 m. These results may provide useful information for ecological research on carbon flux from plankton to benthos in marine ecosystems.