Proteomics, a cutting-edge omics technology, is transforming fish health research by providing molecular insights into pathogen identification, immune responses, and environmental stress adaptations. Advanced proteomic methodologies, particularly mass spectrometry-based techniques such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), have revolutionized the identification of bacterial, viral, and parasitic pathogens while enabling real-time detection of antimicrobial resistance biomarkers. These advancements play a pivotal role in biosecurity strategies and disease mitigation efforts. Beyond pathogen diagnosis, proteomics facilitates a deeper understanding of fish responses to pollutants, stressors, and aquaculture interventions. The emerging field of ecotoxic proteomics provides a molecular fingerprint of aquatic contamination, offering novel biomarkers for environmental monitoring and regulatory frameworks. Moreover, proteomic profiling enhances selective breeding programs by identifying proteins associated with disease resistance, growth performance, and metabolic efficiency, paving the way for precision aquaculture. Integrating proteomics with multiomics approaches including genomics, transcriptomics, and metabolomics has further strengthened aquaculture sustainability, improving vaccine development, immune modulation strategies, and dietary optimization. As aquaculture scales up to meet the rising global protein demand, proteomics emerges as a cornerstone for sustainable fish farming, bridging the gap between aquatic health management and food security.