Urban lagoons are increasingly common features of contemporary cities, frequently created or heavily modified by urban planning and subsequently exposed to chronic anthropogenic stress. Operating far from historical reference conditions, these systems often persist over long periods as novel urban ecosystems. Understanding how ecological functioning is maintained under such conditions is essential for sustainable urban management and resilience planning. We analyzed a highly impacted urban lagoon in Gualeguaychú city, Argentina, using long-term ecological monitoring data (2015–2019), including phytoplankton, zooplankton, benthic macroinvertebrates, fish, and physicochemical variables. Structural (taxonomic) and functional (trait-based) food webs were constructed to evaluate whether ecosystem functioning persists through non-random reorganization rather than structural complexity. Network metrics were compared with degree-preserving null models, and environmental drivers were assessed using correlation analyses and a parsimonious piecewise structural equation model. Results showed pronounced taxonomic simplification and trophic truncation, with communities dominated by pollution-tolerant, benthic-oriented guilds and limited pelagic consumers. Structural networks were simplified and largely indistinguishable from null expectations. In contrast, functional networks exhibited significantly higher modularity, connectance, and redundancy than expected by chance, indicating compensatory organization and energy canalization through detrital, periphytic, and mixotrophic pathways. A minimal physicochemical cascade (Alkalinity → pH → Dissolved Oxygen → Average Trophic Level) revealed the combined role of chemical buffering and functional redundancy in sustaining trophic organization under chronic stress. These findings suggest that urban lagoons may operate as “extreme-by-design” systems, in which persistence arises from constrained yet non-random functional organization rather than from taxonomic richness. From a sustainability perspective, our results support prioritizing functional indicators, such as redundancy, modularity, and basal-resource pathways, over species-based targets when managing chronically disturbed urban aquatic ecosystems.