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Mangrove‐fringed estuaries are intertidal ecosystems discharging significant amounts of dissolved organic matter (DOM) into coastal oceans. DOM in these ecosystems is derived from autochthonous production, fluvial input, and mangrove porewater outwelling; however, differentiating between these sources remains challenging. Our incomplete understanding of the biogeochemical factors controlling DOM dynamics and its relationship with nutrient and trace metal cycling still hinders the formulation of elemental budgets in coastal environments. Here, we relate the DOM composition in a mangrove‐fringed estuary in North Brazil (Amazonia) to the redox conditions at the formation sites. We combined molecular DOM analyses via ultrahigh‐resolution mass spectrometry (FT‐ICR‐MS) with parallel factor analysis of excitation–emission fluorescence matrices (EEM‐PARAFAC), nutrient and redox‐sensitive trace metal analyses. During low tide, the influx of oxygen‐depleted porewater carried terrigenous DOM, inorganic nutrients, and trace metals into the mangrove‐fringed creeks. Precipitation of metal(hydr)oxides and microbial turnover controlled nutrient and trace metal dynamics in the estuary. The highest inorganic nitrogen concentrations within the upper mangrove‐fringed estuary indicated outwelling from mangrove sediments as an essential source. Phosphate concentrations were highest within the lower mangrove‐fringed estuary, where available phosphate likely exceeded precipitation with iron(hydr)oxides. We tracked the DOM transport to the coastal ocean using a novel molecular index derived from sulfidic porewater (ISuP). Outwelling of recalcitrant DOM from mangrove habitats is relevant in the context of blue carbon storage. Therefore, applying our molecular proxy (ISuP), together with trace‐metal and optical DOM analyses, is a powerful approach for differentiating contributions of diverse DOM sources in highly complex coastal ecosystems. [ABSTRACT FROM AUTHOR]