A study on the Pb(II) imprinting performed within mesoporous sulphated biopolymer/siloxane composites, prepared in media containing deep eutectic solvent (DES), is described. In general, the process of imprinting resulted in greatly increased surface areas relatively to the corresponding nonimprinted composites [up to fivefold (from 76 m2 g−1 to 360 m2 g−1) for fucoidan (Fuc) and up to twofold (from 208 m2 g−1 to 351 m2 g−1) for chondroitin sulfate (CS) composites], the diminishing of mean pore size (from 3.3–4.6 nm to 2.9–3.4), and higher biopolymer contents (from mass fractions of 0.42–0.52 to 0.46–0.68). The sorption features depended a great deal on the biopolymer/DES combination. The best CS composite, allowed for 12% capacity and 20% binding strength, as well as Pb(II)/Cd(II) selectivity enhancements. The largest of the capacities was obtained with the imprinted Fuc/DES‐E composite, 86 mg g−1, a 10% increase. Concerning the selectivity [Pb(II) versus Cd(II)], there was a significant increase for the CS composites (from 1.0–1.1 (αqmax)/1.1–1.2 (αK) to 1.3–1.4 (αqmax)/1.3–1.6 (αK)]. In particular, the DES‐E CIC presented high selectivity factors (αqmax 3.0/αK 3.2) in line with those of the microporous version (αqmax 2.0/αK 3.3) but showing a significant increase in terms of the αqmax selectivity. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2020, 137, 48842.