This study examined the effects of humic acid (HA) properties on the equilibrium sorption of phenanthrene. A bulk HA sample based extracted from a peat was fractionated into eight subsamples using an ultrafiltration apparatus with membranes having seven molecular cut-offs. The eight HA fractions obtained have apparent molecular sizes of <1, 1–3, 3–5, 5–10, 10–30, 30–100, 100–300 and >300 kDa, respectively, and their molecular size distributions were further calibrated using high performance size exclusion chromatography (HPSEC). The chemical and structural properties of the eight HA fractions were characterized systematically using different chemical and spectroscopic methods. The equilibrium sorption was measured for the eight HA fractions using phenanthrene as the sorbate. The results showed that the fractions with lower molecular weights had more heterogeneous functional groups, greater O/C atomic ratios, and higher contents of oxygen and lignin-derived aromatic structural units. Conversely, the HA fractions with higher molecular weights had lower contents of oxygen and aromatic structural units that corresponded to greater H/C and lower O/C atomic ratios. The measured sorption isotherm nonlinearity and the sorption capacity correlated well with the size and the chemical properties of the HA macromolecules.