Seagrass meadows are important shallow-water ecosystems that provide habitat for numerous associated organisms and play a crucial role in nutrient cycling, but their detection in the fossil record is problematic. Indirect indicators are often needed to discriminate seagrass beds from other shallow marine paleohabitats. Here, the stable isotope signatures of mollusk shells are examined to determine if they might provide such an indicator in addition to the faunal composition of mollusk assemblages. Aragonitic shells of 167 gastropods and bivalves from Burdigalian and Tortonian deposits in Java and East Kalimantan (Indonesia) are analyzed for their δ18O and δ13C ratios. The faunas represent fully marine to brackish water environments and include seagrass meadows (with dispersed corals), mixed seagrass-coral, and coral-dominated habitats (with dispersed seagrass). We assess processes and settings that shape inorganic isotope signals in the Miocene ambient waters and fractionation processes occurring at the time of shell deposition. Depleted δ18O and δ13C ratios are shown in brackish water samples. Furthermore, chemosymbiotic species show depleted δ13C ratios. A significant difference is found between the carbon isotopic signatures of coral- and seagrass-dominated environments within a stratigraphic interval. Seagrass communities consistently yield comparatively enriched δ13C ratios. Hence, stable isotope ratios may provide additional evidence for distinguishing paleoenvironments and are helpful in identifying ecological processes and settings within these environments.