Identifying patterns and understanding the processes associated with Marine and Coastal Protected Areas (MCPAs) (local scale) are essential for developing specific hypotheses about trophic interactions and potential cascading effects of local and global changes. This can also serve as an initial step in the identification of biodiversity patterns and biological interactions on a regional scale. This study characterized a set of species/taxa composed of four subcommunities featuring macrobenthic infauna, epibenthic megafauna, birds, and mammals observed between 2019 and 2021 in the estuarine and marine system of the Pitipalena-Añihué MCPA in Chilean Patagonia. Biodiversity patterns were analyzed using multidimensional models and indices.A pool of 276 taxa were observed within the studied subcommunities, and reproduction was confirmed for several bird and mammal species (mostly on islets). The results indicate a system with several types of habitats, where the sea lion Otaria flavescens was dominant among the group of marine mammals. Notably, birds and epibenthic megafauna showed differences between the marine and estuarine environment. The observed biodiversity patterns can be attributed to environmental heterogeneity, as well as anthropic effects (including invasive species, fishing, and aquaculture). This work proposes a synthesized spatial distribution scheme of the main taxa, complemented by a matrix of hypothetical trophic interactions. Along with demonstrating the current lack of available information, this matrix offers an opportunity to assess the ecosystem's sensitivity, identify relevant information gaps, and develop hypotheses about specific trophic interactions (scalable to the region) and the potential cascading effects of ocean changes.