Changes imposed to nature by human activities and related impacts on all environmental matrices have become a critical issue. Gradually, humans began to perceive and face the magnitude of the impact of human economy on natural ecosystems and the implications for human well-being. From this perception, the concepts of natural capital and ecosystem services arose, highlighting the relationships between natural and human economy while boosting environmental conservation and management. In this framework, the definition and application of metrics and models capable of accounting for natural capital value are much needed. This is even more important when a protection regime is established (such as in the case of marine protected areas) to evaluate the efficacy of undertaken conservation measures. In this study, a biophysical and trophodynamic environmental accounting model was developed to assess the value of natural capital in marine protected areas. The model of natural capital assessment is articulated in three main steps: 1) trophodynamic analysis, providing an estimate of the primary productivity used to support the benthic trophic web within the study area, 2) biophysical accounting, providing an estimate of the biophysical value of natural capital by means of emergy accounting, and 3) monetary conversion, expressing the biophysical value of natural capital into monetary units. This conversion does not change the biophysical feature of the assessment, but instead it has the merit of allowing an easier understanding and effective communication of the ecological value of natural capital in socio-economic contexts. Keywords: Natural capital, Marine protected areas, Environmental accounting, Benthic habitat, Emergy.