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Ecosystem macroscopic properties given by Ascendency theoretical framework were compared between two multispecies mass-balanced trophic models of the coastal benthic ecosystem along Mejillones Bay in northern Chile (SE Pacific). The models were constructed with a similar number of components representing system conditions for years 2006 and 2018 using Ecopath with Ecosim (EwE) software. The most relevant change was that the macroalgae (principally Rhodophyta group) increased notably over 12 years. In terms of Ascendency, the larger increase in Total System Throughput (TST) compared to the null increment in the Average Mutual Information would indicate that the benthic ecosystem of Mejillones Bay is moving towards eutrophic conditions. This is consistent with the reduction in the TST cycled, Finn's cycling index, and a two-fold increase in the flow of detritus. Likewise, the Keystone Species Complex seems to be sensitive to changes in the properties of ecosystems, reducing the number of components in cases of deteriorated ecosystem. Based on the results obtained, it is suggested the implementation of management strategies that allow reversing this trend towards eutrophication, such as, to strengthen environmental policies and monitoring programs in order to conserve the benthic communities of Mejillones Bay. [ABSTRACT FROM AUTHOR]