The southern part of the tropical Cayo Coco Island (Cuba) hosts a complex, highly evaporative and marine-fed lagoonal network. In the easternmost lagoon of this network, hypersaline conditions favour the development of complex sedimentary microbial ecosystems within the water column at the bottom water-sediment interface and on the shore. Some of these ecosystems are producing microbial mats and biofilms with variable mineralisation rates, depending on their location. Since the mineralisation of these microbial deposits is rare, the sedimentary record does not provide a direct window on the evolution of these ecosystems or their distribution through space and time. However, microbial deposits also produce copious amounts of organic matter, which may be used to decipher any microbial-related origin within the sedimentary record. Microbial mats and biofilms were identified as the potential source of organic material in addition to the surrounding mangrove, soils and suspended particulate matter (SPM). The origin and evolution of the sedimentary organic matter preserved within the lagoonal sediments has been analysed using geochemical parameters such as elemental (TOC, TN and [C/N]atomic ratio) and isotopic (δ13Corg and δ15NTN) signals on four sedimentary cores retrieved from different locations in the lagoon and compared with the geochemical signatures of the potential sources. Despite the high potential for organic matter accumulation in the studied lagoon, the TOC and TN downcore values in sediments that were analysed (i.e., micritic muds and bioclastic sands) remain very low compared to the sediment-water interface. The relative contributions of the different potential sources of organic matter were estimated using [C/N]atomic ratios and δ13Corg values. The δ15NTN signature was discarded as a source signature as it records synsedimentary, early diagenetic, secondary evolution of the nitrogen signal associated with OM remineralisation (i.e., denitrification). Finally, among the microbial deposits, the slime recognised in the permanently submersed zone of the waterbody appears to be the main contributor to the organic matter preserved within the sediments of the lagoon. SPM, mainly composed of microbial-rich particles, also contribute and cannot be ruled out as a source.