Dissolved organic matter and its colored component, Colored Dissolved Organic Matter (CDOM), play a major role in global carbon budgets, and their fluxes provide an essential link between terrestrial and aquatic biogeochemical cycles. Satellite observations can uniquely capture the hydro‐biogeochemical connectivity of terrestrial and aquatic landscapes, across scales. Yet, accurate satellite retrievals of CDOM and dissolved organic carbon (DOC) dynamics remain challenging in urbanized estuaries and coasts. Here, we present an advanced unified algorithm for space‐based retrieval of coastal CDOM and DOC dynamics and its application in Long Island Sound—one of the world's most heavily urbanized estuaries that is becoming increasingly vulnerable to climate change stressors. A rich bio‐optical data set, encompassing a wide range of environmental conditions, was integrated into the algorithm training to retrieve DOC concentrations and CDOM spectral shape (i.e., spectral slope S275–295)—a proxy for DOC quality. The new algorithms were applied to full‐resolution satellite imagery from the Sentinel‐3 Ocean and Land Color Instrument (OLCI) after thoroughly evaluating the performance of six ocean color atmospheric correction approaches (ACOLITE, BAC, C2RCC, MUMM, l2gen, and Polymer). Evaluation of the algorithms yielded mean absolute percent differences of 28%, 12%, and 10% for aCDOM(300), S275–295, and DOC, respectively. Application of the algorithms to multi‐year satellite OLCI imagery captured, for the first time, the coupled impact of seasonal transitions, wind regimes, freshwater inputs, anthropogenic disturbances, and hydrological extremes (both intense precipitation and droughts) on DOC fluxes and CDOM quality at the ecosystem scale. Results have important implications for improved predictions of coastal biogeochemical fluxes in complex urban−estuary systems. Plain Language Summary: Accounting for more than half of the total organic carbon export from land to oceans, dissolved organic carbon (DOC) provides a critical link between terrestrial and aquatic ecosystems. Earth observations from the vantage point of space can uniquely capture the hydrological and biogeochemical connectivity of terrestrial and aquatic landscapes, across spatiotemporal scales. However, accurate satellite retrievals of DOC and its colored component (CDOM) remain challenging in urbanized estuaries impacted by anthropogenic—both air and water—pollution and transient forcings. Here, we present an advanced, generalized algorithm for space‐based retrieval of coastal CDOM and DOC dynamics across different estuarine systems. After thorough evaluation of satellite imagery and its atmospheric correction, we applied this algorithm to examine carbon dynamics in Long Island Sound—one of the world's most urbanized estuaries that is particularly vulnerable to coastal hazards and climate change. Using multi‐year satellite imagery, we were able to capture, for the first time, the coupled impact of winds, riverine discharge, human activity, and extreme events (heavy storms and intense droughts) on DOC fluxes and CDOM quality at the larger ecosystem scale. This research is important for improving our understanding of the response of complex urban ecosystems to future pressures. Key Points: High performance of unified algorithms for satellite retrieval of both dissolved organic carbon (DOC) amount and quality across complex estuaries and river plumesOcean and Land Color Instrument satellite retrievals resolve biogeochemical gradients, from the urban land−water interface to the larger ecosystem scaleRiver discharge, wind regimes, and extreme events (both extreme precipitation and droughts) modulate estuarine DOC fluxes and quality [ABSTRACT FROM AUTHOR]