Estuarine sediments provide a valuable record of changing environmental conditions over time, although deciphering this record can be confounded by dramatic changes in sediment deposition and resuspension, and the effects of bioturbation and microbial degradation. Lipid biomarkers are commonly abundant in estuarine sediments and can provide valuable information on the sources of organic matter and how it is degraded and recycled. Terrestrial organic matter usually predominates and it is mostly derived from transport and deposition of soil-derived material. Biomarkers for this soil-derived organic material include long-chain n-alkanes, n-alkanols, n-alkan-2-ones, triterpenoids and constituents of cutin and suberin including fatty acids, omega-hydroxy fatty acids and alpha,omega-dicarboxylic acids (originally present as esters), and cell wall constituents including sterols and triterpenoids and lastly glycerol dialkyl glycerol tetraethers (GDGTs). Aquatic organic matter is typically characterized by high abundances of sterols, fatty acids and GDGTs, and variable amounts of specific algal markers including long-chain C-37-C-40 alkenones, C-28-C-32 alkyl diols, C-20, C-25 and C-30 highly branched isoprenoid alkenes, chlorophylls and carotenoids. This chapter reviews the application of these various compounds as source-specific biomarkers and investigates the range of degradation reactions that need to be considered when using them as quantitative markers for organic matter inputs.