The Visayan Sea is one of the major traditional fishing grounds in the Philippines and is likewise considered as a top contributor to the country’s overall fisheries production. However, fisheries surveys conducted over the past couple of decades have documented changes in the abundance and composition of catches and stocks toward an increasing dominance of invertebrates and low trophic levels fish families. Assessments of the commercially-important pelagic and demersal stocks were used to estimate population parameters that already exceed the sustainable reference limits. These traditional assessments point exclusively to fishing as the likely cause of the observed status and trends, but they fail to incorporate the potential influence of trophic interactions and variable environmental conditions despite a nationally-legislated mandate to apply an ecosystem approach to assessing and managing the country’s fisheries. Thus, an ecosystem model (Ecopath with Ecosim) of the Visayan Sea was constructed to investigate the role and extent of the fishery, trophic interactions, and changing environmental conditions as drivers of stock abundance and ecosystem dynamics. The results suggest that fishing and its corresponding trophic effects are the major drivers of invertebrate and fish biomass and catches in the Visayan Sea over the past two decades, while the environmental trends provide explanations for patterns that cannot be explained by fishing alone. Incorporating sea surface temperature variations and primary productivity anomalies produced the best-fitting models for most of the observed biomass and catch trends. The catches of the small pelagics (i.e., sardines and mackerels) were likewise found to be particularly affected by rainfall, while the biomass and catch of the small demersal fishes also show a sensitivity to chlorophyll-a concentrations. The primary productivity anomalies further showed a significant correlation with the Pacific Decadal Oscillation (PDO), which suggests that bottom-up trophic controls in the system may be affected by long-term regional climatic changes. These findings validate the applicability and necessity of the ecosystem modeling approach in assessing exploited marine ecosystems to complement the analyses from typically single-species population assessments, especially in the face of increasing environmental variability and projected climate change scenarios.