Mangrove ecosystems can potentially and indirectly modulate the effects of sea level rise due to their ability to trap and retain sediments. In order to gain a better understanding of the potential sediment sources and dynamics in the mangroves of Vanga, Kenya, inter-seasonal riverine, estuarine and coastal/marine sediments together with agricultural soil and mangrove tissues were studied. Elemental ratios (C/N) and carbon (δ13C) stable isotope composition, were analysed to disentangle sources of sediment organic matter (SOM) in the Vanga, Estuary. The organic carbon (C) content, C/N ratios and δ13C values ranged between 0.1 and 2.4%, 9.9 to 35.5 and −24.8 to −19.9‰ respectively. These contents were also as expected relatively higher in mangrove tissues than in all the sediment samples. δ13C values of mangrove sediments were higher than those of the mangrove tissues, which was attributed to rapid decomposition, dilution by freshwater and mineral organic matter (OM) discharged by the Umba River as well as outwashing by ebb tides. On average, C/N ratios were also observed to be greater than 10 in all samples collected during both the dry and wet season. This has been shown to reflect a pronounced contribution of allochthonous organic matter. Using a combination of δ13C values and C/N ratio, the dominance of riverine POM was also evident from a Bayesian Stable Isotope Mixing Model in R-program (SIMMR) that indicated OM source mixing but with a dominant (∼60%) contribution of riverine OM. The observed and modeled variability of SOM in the Vanga estuary points to the hypothesized influence of the Umba River on Vanga Estuary sediments but with evidence of potential material exchange and influence of tidal fluxes within the estuary.