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Abstract: Defining trophic relationships among species is essential for understanding the capacity of marine ecosystems to buffer external perturbations and sustain the flow of energy and nutrients through ecological communities. Yet, most trophic categorizations and food web models are limited by coarse data resolution, limiting reliable projections of food web structure and energetic pathways under anthropogenic stress. DNA metabarcoding and stable isotope analysis are complimentary methods that provide unprecedented resolution of trophic interactions, permitting (1) the reconstruction of complex trophic networks, (2) the evaluation of trophic responses to global change, and (3) the characterization of energy flow in coastal marine systems across the globe. First, I construct one of the highest resolution food webs ever assembled for a coral reef ecosystem, revealing fine-scale partitioning among species. These findings emphasize the importance of examining fish diet beyond broad trophic categories and highlight the vulnerability of trophic specialists to global change. Second, following a coral bleaching event, I examine shifts in feeding behavior and nutrient acquisition in coral reef fishes that are extreme trophic specialists. While these specialists do not alter their feeding preferences, they exhibit reduced nutrient assimilation, demonstrating how recurrent disturbances can have adverse impacts on energetic pathways. Finally, in a global analysis of coastal marine ecosystems, I combine particulate organic matter and environmental DNA analyses to examine how energy quality and quality structure biodiversity. Across taxa and regions, higher energy quality – but not quantity – predict increases in species richness. Together, these findings reveal that the structure, stability, and diversity of marine ecosystems depend on how energy is partitioned and transferred through trophic networks.