The increasing complexity of industrial wastewater, particularly from textile and pharmaceutical industries in the United States, necessitates advanced treatment technologies capable of simultaneously removing multiple dye pollutants. Silica-based hybrid materials have emerged as promising adsorbents due to their high surface area, tunable porosity, chemical stability, and ease of functionalization. This review synthesizes recent advances in synthesis strategies, adsorption mechanisms, and synergistic effects in multi-component dye systems. Particular emphasis is placed on competitive and cooperative interactions, determinants of selectivity, and modeling frameworks that regulate adsorption in complex mixtures. Structure–performance relationships are critically assessed in terms of crystallinity, porosity, and surface chemistry, while optimization strategies underscore the importance of response surface methodology, process intensification, and machine learning in scaling up treatment. Regeneration and reusability studies highlight the economic feasibility of silica-based hybrids, supported by techno-economic and life cycle assessments that demonstrate the environmental benefits of bio-based precursors and integration into circular economy practices. Emerging directions, including pH- and temperature-responsive hybrids, adsorption–photocatalysis integration, and digital twin optimization, further underscore the potential of these materials for next-generation water treatment. This review consolidates both fundamental insights and practical implications of silica-based hybrid adsorbents, advancing their translation from laboratory research to real-world industrial wastewater management.