Organic carbon occluded in diatom silica is assumed to be protected from degradation in the sediment. δ13C from diatom carbon (δ13C(diatom)) therefore potentially provides a signal of conditions during diatom growth. However, there have been few studies based on δ13C(diatom). Numerous variables can influence δ13C of organic matter in the marine environment (e. g., salinity, light, nutrient and CO2 availability). Here we compare δ13C(diatom) and δ13C(TOC) from three sediment records from individual marine inlets (Rauer Group, East Antarctica) to (i) investigate deviations between δ13C(diatom) and δ13C(TOC), to (ii) identify biological and environmental controls on δ13C(diatom) and δ13C(TOC), and to (iii) discuss δ13C(diatom) as a proxy for environmental and climate reconstructions. The records show individual δ13C(diatom) and δ13C(TOC) characteristics, which indicates that δ13C is not primarily controlled by regional climate or atmospheric CO2 concentration. Since the inlets vary in water depths offsets in δ13C are probably related to differences in water column stratification and mixing, which influences redistribution of nutrients and carbon within each inlet. In our dataset changes in δ13C(diatom) and δ13C(TOC) could not unequivocally be ascribed to changes in diatom species composition, either because the variation in δ13C(diatom) between the observed species is too small or because other environmental controls are more dominant. Records from the Southern Ocean show depleted δ13C(diatom) values (1-4 ‰) during glacial times compared to the Holocene. Although climate variability throughout the Holocene is low compared to glacial/interglacial variability, we find variability in δ13C(diatom), which is in the same order of magnitude. δ13C of organic matter produced in the costal marine environment seems to be much more sensitive to environmental changes than open ocean sites and δ13C is of strongly local nature. © 2012 Springer Science+Business Media B.V.