Mangroves located along coastal margins are long-term carbon sinks with higher organic carbon stocks than terrestrial forests. Tracing the different sources of organic matter and its fate in mangrove forests is a complex process because of rapid changes driven by natural and anthropogenic processes. In this study, we trace the distribution and sources of organic matter in six Pb-210-dated sediment cores (200-650 cm in length) collected along a N-S transect from the Rufiji Delta mangrove-estuarine complex in eastern Tanzania. The sampling locations had different tree cover, soil types, and underwent variable natural (fluvial discharge, transport, and early diagenetic post-depositional alterations) and human-induced anthropogenic changes. We investigated C:N ratio, stable carbon and nitrogen isotope compositions, and source-specific diagnostic biomarkers (i.e. fatty acids and n-alkanes) trends to examine these changes in spatial and temporal contexts. In these cores, the average C:N values ranged between 12.7 +/- 0.3 and 22 +/- 2.9 indicating deposition of both terrestrial and marine organic matter that is influenced by its geographic location. The delta N-15 value varied from 0.1 parts per thousand to 4.3 parts per thousand; the more positive values in younger sediments imply anthropogenic inputs. Stable carbon isotope (delta C-13) ranged from -28.6 to -20.5 indicating a dominant terrestrial input. The organic matter sources in sediments were further established based on various biomarker indices. The biomarker data indicated that organic matter is mainly derived from recycled matter and/or marine microorganisms in the northern part of the delta. The central and southern parts of the delta showed a different trend indicating predominantly the presence of land-derived sedimentary organic matter. Organic matter signals in the northern and central parts of the delta indicated the presence of more anthropogenic input, compared to the pristine southern part of the delta. This is due to the proximity of the sites to human settlements, agricultural activities, and inland transport associated with fishing and recreational activities. Finally, our results indicate a low carbon accumulation rate in most parts of the Rufiji Delta compared to the global average. This is driven by the differences in environmental settings and conditions such as sediment dynamics and hydrodynamic transport, vegetation cover, and diagenetic changes at specific sites.