Quantifying the spatiotemporal heterogeneity of sediment nitrogen (N) cycling remained a grand challenge in complex river-dominated margins. Here, we elucidate a universal “pigment pump” mechanism governing sedimentary denitrification across the fluvial-estuarine-marine continuum. Based on a high-resolution survey of 429 sampling stations in the Yangtze River Estuary, we quantified an annual sedimentary denitrification flux of 2.7 × 10⁶ t N yr⁻¹. We demonstrated that algal blooms acted as a primary electron donor source, fueling heterotrophic denitrification while concurrently modulating nitrous oxide (N₂O) release pathways. Comparative analyses spanning diverse systems—including the Changjiang, Pearl, and Aransas-Copano estuaries—confirmed that pigments serve not merely as proxies for environmental variables but as direct, quantifiable drivers of N transformation. This single-parameter dependency enabled high-precision flux modeling. Furthermore, we identified distinct regulatory regimes: turbidity-chlorophyll coupling suppresses N removal in estuarine turbidity maxima, whereas a synergistic effect between mild hypoxia and algal inputs enhanced N removal in mariculture ecosystems. Our findings provided a mechanistic framework that transcended traditional multi-parameter limitations, offered new paradigms for mitigating coastal eutrophication and N₂O emissions.