The analysis of high-resolution stratigraphic data from the Cenomanian-Turonian successions in three sections from Sinai (northeast Egypt) revealed the mechanisms behind water depth-driven biological responses (visible in changes of biodiversity and community structure) of macroinvertebrates. Quantitative biostratigraphical analysis of 127 samples containing 6203 specimens representing 41 genera of molluscs, corals, and echinoids were used to construct changes in the community structure of Cenomanian-Turonian macroinvertebrates. We identified six assemblages that we assigned to two main categories and linked to regional sea-level changes. The first group of assemblages is associated with the initiation of transgression and/or late normal regression, is dominated mainly by opportunistic, epifaunal suspension feeders (oyster bivalves) and is characterized by lower diversity values (low Shannon Index and high dominance). The second category is associated with the maximum flooding zone and dominated by infaunal deposit feeders such as irregular echinoids and by nektonic ammonites and is characterized by higher diversity. The increase in nektonic and decrease in benthic taxa during the latest Cenomanian suggest deepening of the environment. Moreover, the change in the water depth was accompanied by a change in the structure of the macrobenthos.