The significant environmental issue of water pollution caused by emerging contaminants underscores the imperative for developing novel cleanup methods that are efficient, economically viable, and that are intended to operate at high capacity and under continuous flows at the industrial scale. This study shows the results of the operational design to build a prototype for the retention at lab scale of pollutant residues in water by using as adsorbent material, insoluble polymers prepared by β-cyclodextrin and epichlorohydrin as a cross-linking agent. Laboratory in-batch tests were run to find out the adsorbent performances against furosemide and hydrochlorothiazide as pollutant models. The initial evaluation concerning the dosage of adsorbent, pH levels, agitation, and concentration of pharmaceutical pollutants enabled us to identify the optimal conditions for conducting the subsequent experiments. The adsorption kinetic and the mechanisms involved were evaluated revealing that the experimental data perfectly fit the pseudo second-order model, with the adsorption process being mainly governed by chemisorption. With KF constant values of 0.044 (L/g) and 0.029 (L/g) for furosemide and hydrochlorothiazide, respectively, and the determination coefficient (R2) being higher than 0.9 for both compounds, Freundlich yielded the most favorable outcomes, suggesting that the adsorption process occurs on heterogeneous surfaces involving both chemisorption and physisorption processes. The maximum monolayer adsorption capacity (qmax) obtained by the Langmuir isotherm revealed a saturation of the β-CDs-EPI polymer surface 1.45 times higher for furosemide (qmax = 1.282 mg/g) than hydrochlorothiazide (qmax = 0.844 mg/g). Based on these results, the sizing design and building of a lab-scale model were carried out, which in turn will be used later to evaluate its performance working in continuous flow in a real scenario.