Wastewater-based epidemiology (WBE) has proven to be a powerful tool for urban health surveillance, offering real-time and community-level insights into public health through sewage biomarker analysis. During the COVID-19 pandemic, WBE has been shown to detect SARS-CoV-2 RNA prior to clinical case surges, and therefore facilitate timely interventions and resource allocation. Our recent study in Taiwan applied a One Health approach to monitor rodent-borne pathogens, such as Leptospira interrogans, hantaviruses, and rat hepatitis E virus. Wastewater was sampled in Tamsui District, New Taipei, monthly between June 2023 and May 2024, and 38.2% of the samples tested positive, with Leptospira found in 36.6% of the samples, including treated effluents. Genetic sequencing showed that the detected bacteria were similar to strains in rodents and human cases, highlighting their environmental persistence and zoonotic potential. Notably, pathogen detection often preceded or occurred without reported human cases, which may suggest underdiagnosis. Complementary pilot studies in Taoyuan and Kaohsiung further demonstrated WBE’s capacity to detect adenovirus, Francisella spp., and rodent DNA, revealing dynamic urban zoonotic risks influenced by rainfall and geography. WBE aligns with Sustainable Development Goals (SDGs) 3, 6, and 11 by enabling ethical, inclusive, and cost-effective health monitoring without individual-level data. Its integration into urban planning enhances resilience, supports early warning systems, and informs equitable public health strategies. This study illustrates WBE’s strategic role in building SDG-aligned healthy cities and calls for cross-sectoral collaboration to scale its implementation.