Abstract. Organic matter (OM) exchanges between adjacent habitats affect the dynamics and functioning of coastal systems, as well as the role of the different primary producers as energy and nutrient sources in food webs. Elemental (C, N, C : N) and isotope (δ13C) signatures and fatty acid (FA) profiles were used to assess the influence of geomorphological setting in two climatic seasons on the export and fate of mangrove OM across a tidally influenced tropical area, Gazi Bay (Kenya). The main results indicate that tidal transport, along with riverine runoff, plays a significant role in the distribution of mangrove organic matter. In particular, a marked spatial variability in the export of organic matter from mangroves to adjacent habitats was due to the different settings of the creeks flowing into the bay. Kinondo Creek acted as a mangrove retention site, where export of mangrove material was limited to the contiguous intertidal area, while Kidogoweni Creek acted as a flow-through system, from which mangrove material spreads into the bay, especially in the rainy season. This pattern was evident from the isotopic signature of primary producers, which were more 13C-depleted in the Kinondo Creek and nearby, due to the lower dilution of the dissolved inorganic carbon (DIC) pool, typically depleted as an effect of intense mangrove mineralisation. Despite the trapping efficiency of the seagrass canopy, suspended particulate OM showed the important contribution of mangroves across the whole bay, up to the coral reef, as an effect of the strong ebb tide. Overall, mixing model outcomes indicated a widespread mixed contribution of both allochthonous and autochthonous OM sources across Gazi Bay. Moreover, FAs indicated a notable contribution of brown macroalgae and bacteria in both sediment and suspended pools. These results suggest that ecological connectivity in Gazi Bay is strongly influenced by geomorphological setting, which may have far-reaching consequences for the functioning of the whole ecosystem and the local food webs.