Compositional changes in dissolved organic matter (DOM) matrix via solid phase extraction (SPE) remain under-constrained due to disproportional extraction of specific groups of compounds. This study elucidates changes in the composition of DOM via SPE by presenting an intercomparison of recovery efficiencies of dissolved lignin phenol standards using three SPE cartridges (C-18, PPL and HLB) and an intercomparison of free-lignin phenols and lignin-oxidized products (LOPs) (via SPE) for two end-members (river and coastal) in the Suwannee River, Cedar Key, Florida. A comparison was also made between DOC and dissolved lignin recovery rates, fluorescence intensity, EEMs indices, spectral slope (SR) and specific UV absorbance at 254 nm (SUVA254) for the river end-members. Isolates harbored lower fluorescence intensities, lower EEMs index values, lower aromatic indices and higher spectral slopes indicating changes in both concentration and composition after SPE. Our results highlight that fractionation is occurring during SPE for lignin-phenol standards, LOPs, and DOM. Riverine end-member DOC extraction efficiencies and dissolved lignin (Σ8) recoveries were 46–60% and 41–48%, respectively, while coastal end-member DOC efficiencies were lower and ranged from to 41% to 47%. In terms of DOC recovery, PPL was the best for river (60%) and coastal (47%), while in terms of LOP recovery, the three cartridges gave comparable results for dissolved lignin and one cartridge type is not necessarily better than the others for coastal samples.