Abstract: The sustainable management of aquatic ecosystems faces growing challenges due to the accumulation of plant-derived biomass waste in polluted lakes and reservoirs. Issues such as impaired plant growth, uncontrolled proliferation, seasonal die-off, and rapid decomposition of vegetation contribute to significant accumulations of organic residues. These materials not only deteriorate water quality by releasing nutrients and accelerating eutrophication but also disrupt the ecological balance of freshwater habitats. Without timely and systematic intervention, such residual biomass can cause secondary pollution, further compromising aquatic biodiversity and ecosystem services. Against the backdrop of China’s Zero-Waste City initiative, there is a pressing need to transition from conventional disposal methods toward sustainable, resource-oriented strategies consistent with circular economy principles. To address the challenge of selecting appropriate treatment pathways, this study developed a multi-criteria decision framework based on the Analytic Hierarchy Process (AHP). The framework integrates five fundamental dimensions, including technical economic, environmental, social, and policy criteria, supported by 17 sub-criteria that systematically reflect sustainability priorities and local operational conditions. The model was applied to assess typical forms of aquatic waste, such as cyanobacterial blooms and water hyacinth (Pontederia crassipes) in Suzhou City, a representative urban area in China confronting eutrophication and aquatic vegetation management challenges. The AHP-based weighting results highlighted technical feasibility as the most influential criterion, accounting for 51% of the total decision weight. Among environmental sub-criteria, carbon emissions emerged as a dominant factor with a weight of 17.94%, underscoring the growing importance of low-carbon considerations in technology selection. Using a normalized scoring mechanism, aerobic composting received the highest comprehensive evaluation score (7.215), attributable to its strong compatibility with high-fiber feedstock, steady market demand for compost products, and operational adaptability to local infrastructure. Anaerobic digestion ranked second (6.416), offering appreciable energy recovery benefits though limited by process stability requirements and capital investment. Co-incineration (5.549) scored lower, constrained by its reliance on auxiliary fuels, higher emissions, and public acceptance challenges, positioning it mainly as a contingency option. Based on these findings, the study proposes an integrated and hierarchical management system centered on aerobic composting, supplemented by anaerobic digestion, and incorporating co-incineration as a contingency option. This multi-technology framework is designed to enhance flexibility, resource output, and environmental performance. Further analysis emphasizes the importance of region-specific policy support, industrial symbiosis models, and regulatory incentives to enable technology adoption and scalling. By combining scientific assessment with practical policy insights, this research provides a robust and transferable decision-support tool for advancing sustainable resource utilization of aquatic plant residue in urban and peri-urban contexts.