Community parameters of diatoms have been used as useful bioindicators for bioassessment of both lentic and lotic systems. The influence of enumeration time periods on detecting community parameters of periphytic diatom assemblages within different exposure times was studied using an artificial substratum in coastal waters of the Yellow Sea, northern China, during the period May–June 2010. Samples were collected at a depth of 1 m, and were examined with different enumeration time periods. Enumeration time periods represented a significant influence on detecting the community features of periphytic diatoms, although no significant changes occurred in periphytic diatom community structure between two enumeration schemes (within 24 h and 24–48 h). The delayed enumeration (within 24–48 h) may result in the similarity of the communities being reduced 10–29%, and in species numbers decreasing and in abundance increasing with exposure duration, respectively. The diversity (richness, evenness and diversity of species) indices were significantly decreased in almost all samples with >10% standard errors at some exposure times by the delayed enumeration scheme. These results suggest that the delayed enumeration may have resulted in the species richness and individual abundance of periphytic diatoms significantly decreasing and increasing, respectively, and thus significantly affected the analyses of species diversity for assessing water quality in marine ecosystems.