Sediment organic matter (SOM) plays an important role in capturing polybrominated diphenyl ethers (PBDEs) due to its affinity to hydrophobic and lipophilic compounds. Previous publications about correlations between PBDE concentrations and SOM content showed discrepancies among the results, reporting either significant positive correlations or no correlations at all. This work aimed to provide a deeper insight into SOM characteristics that might determine the concentrations of PBDEs in sediments. Sediment samples from Mendoza province, Argentina, were analyzed to contrast two models, environmental and experimental, using multivariate learning methods. Mendoza has been going through increasing events of drought and water scarcity, hence the occurrence, transport, and fate of contaminants as PBDEs in aquatic environments is of superlative importance. Principal component analysis (PCA) and partial least squares regression (PLS) were used to evaluate the correlations between physicochemical properties of sediments, semi-quantitative Fourier transform infrared (FTIR) area ratios obtained from SOM spectra, and PBDE concentrations in sediments. Moreover, a linear model was proposed to determine SOM density using FTIR area ratios and it was used as an additional variable in multivariate analyses. The results obtained from PCA and PLS were consistent and revealed that PBDE concentrations in sediments were correlated with a more degraded SOM, characterized by shorter and more branched hydrocarbon chains. PBDE concentrations were also correlated with higher SOM density values, which in turn were correlated with SOM degradation. These findings extend previous understanding and emphasize that not only is the organic matter content a factor in determining PBDE concentrations in sediments, but also and more significantly, its degree of degradation.