The geochemical behavior of total organic matter (TOM), total organic carbon (TOC), total nitrogen (TN) and total phosphorus (TP) was evaluated in the surface sediments of West (WB) and East (EB) bays of El Morro de Puerto Santo, as well as the TOC/TN relationship to know the present biogeochemical cycles, which will allow future studies to assess the responses of the ecosystem to anthropic intervention. TN concentrations varied in WB and EB in 464 to 278x103 and 570 to 998 mg/kg, respectively, while TP presented variations between 300-1.04x103 in WB and 72.1-241 mg/kg in EB. Values of TOC, TOM and CaCO3 averaged 2.67, 9.09 and 28.6% respectively in the WB and 0.49, 1.35 and 51.6% in the EB. The Kruskal Wallis analysis showed significant differences between the medians of both bays for the geochemical parameters at a significance level p <0.0001, their maximum concentrations were recorded in the coastal margin and central zone of the WB with little variability between the stations of the WB. The TOC/TN ratio estimated for the WB a mixture of marine and terrestrial sources and strong organic contamination (TOC/TN= 3.76-81.9), while for the EB, the deposition of TOM in sediment is of origin autochthonous (TOC/TNprom = 6.48) associated with coastal upwelling processes. The concentrations and distribution patterns of TN and TP in the sediments are characteristic of the geochemistry of each sedimentary environment and are associated with the anthropic activities developed in its margins.