Interaction with natural organic matter (NOM) is hypothesized to impact the fate and bioavailability of enzymes and some hazardous proteins in terrestrial and aquatic environments. By using saturated column transport experiments the transport and deposition of the model enzyme lysozyme (LSZ), in the absence and presence of purified Aldrich humic acid (PAHA), was investigated at a series of mass ratios PAHA/LSZ at pH 5 and 8 and two ionic strength values (0.5 mM and 50 mM KCl solution). PAHA decreased LSZ transport under all conditions. The shapes of breakthrough curves (BTCs) and retention profiles (RPs) during cotransport of both colloids evolved from symmetrical to blocking with time and from flat to hyper-exponential with depth, respectively, in response to increases in mass ratio PAHA/LSZ. The results indicated that the “size-selective retention” and concurrent homo- and hetero-aggregation induced straining, which resulted in preferential retention of relatively large PAHA-LSZ aggregates in the column and elution of relatively small ones. Due to differences in aggregate size, in general, the enzyme activity of LSZ in the effluent was larger and that of the retained LSZ was smaller than that of the influent. Therefore, protein transport process could partially increase the enzyme activity and bring potential environmental hazards.