This dataset contains geographic coordinates (latitude, longitude in decimal degrees), water depth (m), calcium carbonate content (CaCO₃, %), and total organic carbon content (TOC, %) for 51 inter-reef seafloor surface sediment samples collected across the Spermonde Archipelago, a land-attached tropical carbonate shelf off southwest Sulawesi, Indonesia. Samples were collected along cross-shelf transects spanning nearshore to offshore zones in both northern and southern sectors of the shelf. CaCO₃ was determined by the Scheibler calcimetry method (Müller & Gastner, 1971); TOC was measured following removal of inorganic carbon. These data characterise the bulk geochemical gradient across the shelf and serve as primary environmental proxies for terrestrial input and carbonate production intensity. The field sampling was performed in August 2021 in the framework of the HAnsea project, sample depths range from 4.5 to 73.6 m water depth. Data collection was done between June 2023 and April 2024.