The sedimentary organic matter (OM) of natural origin in the Ria de Aveiro and the estuary of Mondego River was characterized using elemental composition (C and N) and lipid biomarkers (sterols, alcohols and triterpenoids). In addition, the contribution by sewage was evaluated by coprostanol and other fecal sterols. Surface sediment samples were collected at 22 stations along the two regions. The lipid biomarkers was extracted, separated with silica-gel and analyzed by gas chromatography coupled to mass spectrometry. Concentrations of total organic carbon (9.94 and 43.00 mg g(-1)) was highly correlated with total nitrogen (r(2) = 0.86). The C/N molar ratio: 14,34 plus-minus 1,75 are typical values of OM of continental origin. There is a major contribution of terrestrially OM to the sediments, as suggested by proxies, including: predominance of long-chain (greater-than or equal to C22) alcohols, higher abundance of sitosterol, estigmasterol and campesterol over other phytosterols, like cholesterol and brassicasterol, and elevated concentrations of triterpenoids from higher plants, as Beta-amyrin and Alpha-amyrin. The concentrations of coprostanol (0.05 to 16.6 micrograms g(-1)) indicated the presence of sewage in seven stations located in the Largo do Laranjo (S4, S5, S6, S7, S10), Port of Aveiro (S14) and in Ílhavo Channel (S16). The more significant contribution of sewage was identified in the Largo do Laranjo (S8 and S9) and the Port of Mondego (S19).