Tropical shelf seas produce carbonate sediment from shells of small marine organisms, but mud and nutrients from land, carried in during seasonal rains, can disrupt this. We studied seafloor sediment and shell-forming organisms at 51 sites on a shelf in Indonesia to see how land input shapes carbonate production. Sediment composition shifts abruptly with distance from shore, and differs by region, reflecting river influence. Findings may help interpret carbonate sediments in the geological past.