<p>Urbanization is a leading driver of change in freshwater ecosystems worldwide, directly altering biodiversity and ecosystem services. We systematically reviewed how urban ecology examines freshwater ecosystems and organism–environment relationships. We searched databases and synthesized evidence to examine associations among environments, biological groups, and urbanization. We also applied structural topic modeling to identify thematic trends and gaps. Our review indicates that ecosystem degradation and anthropogenic pollution are the most frequently addressed pressures, that rivers predominate in sampling, and that fish, macroinvertebrates, bacteria, and phytoplankton are most commonly studied taxa. Although management, conservation, and ecosystem services are frequently mentioned, they are rarely operationalized. Recurring co-occurrence patterns emerged: plankton with eutrophication; amphibians and aquatic macrophytes with wetlands and ponds; fish and macroinvertebrates with pollution and habitat fragmentation; and bacteria with rivers and public-health impacts. These patterns suggest the literature uses focal taxa as sentinels and is dominated by observational, stressor-focused study designs. This emphasis helps explain recurring pairings but limits generalization across urban freshwater systems. We found heterogeneity in how urbanization is defined and scaled, limiting comparability and causal inference. We propose priorities to standardize urban metrics, expand experimental and longitudinal designs, and strengthen research-management links to inform urban planning and freshwater conservation.</p>