Herein, lipid biomarker analysis is applied to surface sediments from the southeastern Niger Delta region for the quantitative determination of aliphatic lipids, steroids and triterpenoids in order to differentiate between natural (autochthonous vs. allochthonous) and anthropogenic organic matter (OM) inputs to this deltaic environment. This ecosystem, composed of the Cross, Great Kwa and Calabar Rivers, is receiving new attention due to increased human and industrial development activities and the potential effects of these activities impacting its environmental health. While the presence of low molecular weight n-alkanes (<C22) and the fossil biomarkers pristane and phytane in all samples, are indicative of a minor petroleum related input, the total extractable organic component of the surface sediments of these rivers remains predominantly of a natural origin as characterized by the variety and predominance of lipid classes that are mainly derived from the epicuticular waxes of vascular plants and include n-alkanes, n-alkanols, n-alkan-2-ones, n-alkanoic acids, steroids and triterpenoids. In addition, recent OM inputs from microorganisms are indicated by the presence of lower molecular weight n-alkanoic acids (Cmax=16), while the major triterpenoids of the sediments, taraxerol and friedelin, and the major sterol, sitosterol, indicate recent OM inputs from vascular plants. Plankton-derived sterols, such as fucosterol and dinosterol, are also found in sediments from the Cross and Great Kwa Rivers and likely originate from autochthonous primary productivity. Furthermore, the coprosterols coprostanol and 24-ethylcoprostanol are present in most samples and indicate measurable anthropogenic contributions from domestic untreated sewage inputs and agricultural run-off, respectively. Of the three rivers studied, the Cross River system was excessively influenced by human and industrial development activities, including drivers such as urbanization and population center growth, land-use change to support agricultural production and animal husbandry, and petroleum exploration and production. These influences were found to be regionally specific as controlled by point sources of pollution based on the relative distributions measured and on the fact that the molecular characteristics of sedimentary OM were not distributed smoothly along a gradient.