Studies of long-term ecological changes are crucial for understanding the factors that govern the distribution and abundance of taxa in time and space. The present study analyses the long-term patterns of palaeoecological changes during the Late Cretaceous, using the marine bivalve fossil record of the Ariyalur Sub-basin, south India. Multivariate quantitative analyses reveal a conspicuous shift in the bivalve palaeocommunity structure from the middle Turonian–Santonian Garudamangalam Formation to the early Maastrichtian Kallankurichchi Formation. A concomitant decline in diversity and evenness from the Garudamangalam to the Kallankurichchi is also associated with a near disappearance of infaunal groups in the latter, where a few stationary epifaunal taxa exhibit overwhelming dominance. Both formations appear to have suffered taphonomic alteration and lithification bias that may have contributed to the reduction of species diversity. The dominance of shallow burrower bivalves in the siliciclastic-dominated Garudamangalam Formation reflects a scenario comparable to the post-Palaeozoic marine assemblages. In contrast, the development of a firmer substrate (firmground), aided by a possible reduction in the siliciclastic supply during an inferred sea-level rise during the deposition of the Kallankurichchi Formation, was more favourable for epifaunal bivalves. Reduced sedimentation rate may have resulted in a low nutrient environment and the development of firmgrounds that offer the required substrate stability for epifaunal bivalves, but a decrease in infaunal burrowing efficiency in the Kallankurichchi Formation. The worldwide prevalence of recliner bivalves in carbonate and mixed siliciclastic-carbonate systems during the Late Cretaceous underscores the importance of substrate conditions in determining bivalve palaeocommunity structure.