The flocculation of dissolved organic matter (DOM) was studied along transects through three boreal estuaries. Besides the bulk concentration parameters, a suite of DOM quality parameters were investigated, including colored DOM (CDOM), fluorescent DOM, and the molecular weight of DOM as well as associated dissolved iron concentrations. We observed significant deviations from conservative mixing at low salinities (0.2 µm) and thereby removing them from the dissolved phase. We also measured flocculation of CDOM, especially in the UV region of the absorption spectrum. Protein-like fluorescence of DOM decreased, while humic-like fluorescence increased because of salt-induced flocculation. Additionally, there was a decrease in molecular weight of DOM. Consequently, the quantity and quality of the remaining DOM pool was significantly changed after influenced to flocculation. Based on these results, we constructed a mechanistic, two-component flocculation model. Our findings underline the importance of the coastal filter, where riverine organic matter is flocculated and exported to the sediments.