In order to balance the impact of agricultural development on land around coastal lagoons with the protection of aquatic resources, knowledge of the role of the sedimentary phase in the entrapment or availability of nutrients in the water column in areas affected by agroindustrial outlets is important. The Ensenada del Pabellon coastal on the Pacific coast of Mexico was chosen to be analyzed. The input of ammonium and orthophosphate from sediment using semicontrolled benthic chambers near a sugar cane factory outlet was compared to non altered sediment. Phosphate and ammonia loading from agroindustrial outlets has been the primary cause of eutrophication. The inputs of ammonium and orthophosphates from the sediment to the water column depend on their concentration in the agroindustrial outlet's waste water, the local morphology, the tide, and biotic assimilation, in order of importance. Sediment in non-altered revealed maxima of 7.8 mg m−2 d−1 of NH+4 nd 1.4 mg m−2 d−1 of PO−34, whereas in one outlet that greatly transfigures the environment, maxima of 223 mg m−2 d−1 of NH+4 and 67 mg m−2 d−1 of PO−34 were recorded, which represent an increase greater than 20 times the normal diffusion. These figures varied markedly in space and time. Results from the study indicated that existing levels of nutrient could endanger the future of this ecosystem, including its sustainable fisheries.