Herein, we report on the use of chitosan-based engineered materials for the sequestration of naphthenic acid fraction compounds (NAFCs) and other species (matrix) in oil sands process-affected water (OSPW) in order to improve monitoring of NAFCs after phytoremediation. Chitosan pellets (CPs) were cross linked with glutaraldehyde (GLU) at variable feed ratios and characterized using thermogravimetric analysis (TGA). Sorption studies at equilibrium and kinetic conditions were carried on OSPW extract, raw and treated wetland samples. The materials were shown to have similar sorption capacity for NAFCs but with variable selectivity of the species in the complex mixture. As well, the matrix uptake varied according to the type of OSPW. Overall, CP in its native form outperformed the cross linked CP pellets, as evidenced by a reduction in matrix effects.