Dissolved organic matter (DOM) is a crucial component of continental aquatic ecosystems. It plays a vital role in the carbon cycle by serving as a significant source and reservoir of carbon in water. DOM provides energy and nutrients to organisms, affecting primary productivity, organic composition, and the food chain. This study presents empirical bio-optical models for estimating the absorption of colored dissolved organic matter (aCDOM) in the Negro River using in situ remote sensing reflectance (Rrs) data. Physical–chemical data (TSS, DOC, and POC) and optical data (aCDOM and Rrs) were collected from the Negro River, its tributaries, and lakes and empirical relationships between aCDOM at 440 nm, single band, and the ratio bands of Rrs were assessed. The analysis of spectral slope shows no statistically significant correlations with DOC concentration or aCDOM absorption coefficient. However, strong relationships were observed between DOC and aCDOM (R2 = 0.72), aCDOM and Rrs at 650 nm (R2 > 0.80 and RMSE < 1.75 m−1), as well as aCDOM and the green/red band ratio (R2 > 0.80 and RMSE < 2.30 m−1). aCDOM displayed large spatial and temporal variations, varying from 1.9 up to 20.1 m−1, with higher values in rivers of the upper course of the Negro basin and lower values in rivers with total solids suspended > 10 mg·L−1. Environmental factors that influence the production of dissolved organic matter include soil type, dense forest cover, high precipitation, and low erosion rates. This study demonstrated that aCDOM can serve as an indicator of DOC, and Rrs can serve as an indicator of aCDOM in the Negro basin. Our findings offer a starting point for future research on the optical properties of Amazonian black-water rivers.
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