Diagenesis of organic matter in coastal sediments from Long Island Sound (LIS) was investigated by measuring fatty acids and sterols in (1) a time-series of surface sediment samples over a spring phytoplankton bloom; and (2) sediment cores collected during and after a bloom at two sites with distinctively different bottom-water oxygen contents. Time-dependent distributions of sedimentary fatty acids and sterols in LIS were strongly affected by pulsed inputs from the overlying water column, variations in benthic community, and redox-related degradation processes. The phytoplankton bloom delivered an intense pulse of unsaturated fatty acids (e.g., 16:1(ω7) and 20:5) to the surface sediments. Continuous increases of cholesterol and diunsaturated sterols after the bloom were related to zooplankton grazing processes and increase in benthic faunal abundance. High inventories of planktonic fatty acids and sterols in the upper 5 cm sediments were observed at the low oxygen site during summer, probably caused by a combination of higher input, reduced degradation rates and lower macrofaunal activity under anoxic conditions compared to oxic conditions.