Sediment samples were collected from three sea cucumber (Apostichopus japonicus) farming ponds of varying water depths, i.e., low (1#), normal (2#), and high (3#) water level depths, in the mariculture zone of Jinghai Bay from July 2012 to April 2013. Macrobenthic community structures were analyzed to investigate the effects of the changes in water depth. Light intensity, Chlorophyll a (Chla) and total organic matter (TOM) contents differed significantly among the three ponds. Light intensity and TOM content of pond 1# were significantly higher than those of pond 3# in summer, winter, and spring; whereas no significant differences were observed among the three ponds in autumn. Chla content of pond 1# was significantly higher than that of pond 3# in summer, winter, and spring; but significantly lower than that of pond 3# in autumn. No significant differences in water temperature were observed among the three ponds for any of the four seasons. Throughout the investigation, 41 macrobenthic species were identified, of which 21 species were annelids (51.2%), 16 species were mollusks (39.0%) and four species were crustaceans (9.8%). Significant differences in species composition, dominant species, abundance, biomass, and diversity index were observed among the three ponds during each season. Macrobenthic abundance and biomass of pond 1# were significantly higher than those of pond 3# in summer, but significantly lower than those of pond 3# in autumn and winter. In spring, macrobenthic abundance of pond 1# was significantly higher than that of pond 3#, with no significant difference in biomass between the two ponds. These results could be attributed to the remarkable fluctuations in the abundance of the dominant species such as Musculus senhousia, Lumbriconeris heteropoda,Cirriformia tentaculata,Ruditapes philippinarum and Eocylichna braunsi. The Margalef's richness index of pond 1# was significantly higher than that of pond 3# in summer; and the Shannon-Wiener diversity and Pielou's evenness indices of pond 1# were significantly higher than those of pond 3# in autumn. The Margalef's richness index and Pielou's evenness index of pond 3# however, were significantly higher than those of pond 1# in spring. No significant differences in diversity index were observed among the three ponds in winter. Hierarchical cluster analysis based on the Bray-Curtis similarity coefficients revealed that the community structure similarities among the three ponds were 43% in July, 37% in October, 43% in January and 48% in April. The low similarities among the three ponds suggested that the macrobenthic community structures were significantly influenced by differences in water depth. The analysis of similarities (ANOSIM) indicated significant differences in species compositions among the three ponds for each season. The similarity percentages analysis (SIMPER) showed that the species that comprised the macrobenthic communities of different ponds, were also the dominant species in each pond for each season. Canonical correspondence ordination analysis (CCA) showed that water depth, Chla, and TOM contents were the key factors influencing the macrobenthic community structures in summer and winter; whereas water depth, light intensity, Chla, and TOM contents were the key factors affecting macrobenthic community structures in spring and autumn.