The trophic structure of ecosystems, reflecting biomass distribution across different levels, is paramount for understanding energy dynamics and community assemblages in marine environments. Typically, ecosystems devoid of external energy influx exhibit a bottom-heavy trophic pyramid, yet higher biomass systems often display a top heavy or concave distribution. Such structures are susceptible to alterations due to species turnover, trophic cascades, and anthropogenic impacts, particularly the phenomenon of ’Fishing down’ the food web. Recognizing the trophic structure as a simplified yet potent indicator, we identify the necessity for a standardized, expedient method to assess reef health—a criterion fulfilled by our Normalized Reef Status Index (NRSI). The NRSI offers a novel metric for scientists and conservation practitioners to augment traditional reef health assessments. Utilizing the NRSI, we assessed the ecological status of 346 reefs across the Mexican Pacific. Our results demonstrated that only reefs within Fully Protected areas conform to the concave trophic structure indicative of low human interference. In stark contrast, unprotected reefs exhibited a depleted trophic architecture, often devoid of apex predators. This depletion not only threatens coastal livelihoods and food security but also disrupts the delicate balance of marine ecosystems critical to sustaining global ecological functions. Through the NRSI, we provide a robust, scalable tool for ongoing monitoring and conservation efforts, underscoring the urgent need to address human-induced trophic disruptions.