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Abstract Flocculation of riverine dissolved organic matter (DOM) in estuaries is crucial for transforming and removing terrestrial carbon inputs across the land-to-ocean aquatic continuum. We measured variations in chromophoric DOM (CDOM) absorption and fluorescence of riverine DOM through mixing experiments conducted across various seasons and environments, identifying patterns in salt-induced flocculation. Our observations show a systematic reduction in CDOM absorption in the 250–450 nm range at salinity 2, with a sharper decrease at higher wavelengths. Flocculation led to decreased relative fluorescence intensity below emission wavelength of 360 nm and an increased intensity at higher emission wavelengths across the excitation spectrum measured (250–450 nm). We introduce a new metric,red shift ratio, a fluorescence-based metric calculated as the ratio of emission intensity at 300–350 nm to that at 360–500 nm, at excitation wavelengths between 250 and 300 nm, for detecting flocculation-induced changes in CDOM across estuarine systems. The observed sensitivity of CDOM to flocculation in low salinities challenges its use as a conservative tracer in coastal gradients, suggesting that recalibrations are required for remote sensing algorithms and carbon flux estimations across land-sea continuum, particularly in systems with similar characteristics.