Urban aquatic ecosystems, which include rivers, lakes, ponds, wetlands, and coastal waters within or near cities, face a multitude of challenges due to increasing urbanization, industrialization, and population pressures. These ecosystems are critical for maintaining biodiversity, regulating water cycles, providing recreational opportunities, and supporting livelihoods. However, their management in urban areas is complex due to overlapping environmental, social, and economic factors. One of the primary challenges is pollution. Urban areas generate substantial quantities of wastewater from domestic, industrial, and commercial sources. When untreated or partially treated, this wastewater introduces high levels of nutrients, heavy metals, and pathogens into aquatic ecosystems, leading to eutrophication, oxygen depletion, and loss of aquatic species. Nutrient overloading, particularly from nitrogen and phosphorus, stimulates excessive growth of algae, causing algal blooms that disrupt aquatic food webs and degrade water quality. Chemical pollutants from industrial effluents, including toxic compounds and persistent organic pollutants, accumulate in sediments and aquatic organisms, posing long-term ecological and human health risks. Microplastics and other solid wastes from urban runoff further exacerbate pollution, making the water bodies uninhabitable for many species and affecting ecosystem services. Another significant challenge in urban aquatic ecosystem management is habitat degradation. Urban development often leads to the physical modification of rivers, lakes, and wetlands. Channelization of rivers, construction of dams and embankments, reclamation of wetlands, and dredging of water bodies alter natural flow regimes and sediment dynamics. These modifications can destroy critical habitats such as spawning grounds for fish, nesting areas for birds, and refuges for invertebrates. Fragmentation of aquatic habitats reduces connectivity between water bodies, which is essential for the migration of species and maintaining genetic diversity. Urban encroachment often reduces riparian vegetation, which plays a key role in stabilizing banks, filtering pollutants, and providing shade to regulate water temperature. Loss of such vegetation also diminishes the capacity of aquatic ecosystems to absorb excess nutrients and pollutants, further amplifying environmental stress. Water quantity and flow regulation represent another major challenge. Urban areas frequently demand substantial quantities of water for domestic, industrial, and recreational purposes, leading to over-extraction from rivers, lakes, and aquifers. Altered flow regimes from water abstraction or stormwater channeling affect the natural hydrology of aquatic ecosystems, causing reduced water levels, increased sedimentation,