Adsorptive removal and dynamic interaction of three different pharmaceutical pollutants, namely rifampicin (RIF), streptomycin (STM), and ibuprofen (IBU) onto chitosan were systematically investigated using a batch adsorption technique at different processing parameters. In this study, chitosan was derived from mud-crab shells, as an innovative way to use the waste from marine foods as adsorbents. The kinetics, intraparticle diffusion, mechanism, and thermodynamics of the adsorption were systematically evaluated and analyzed using kinetic models, Boyd mass transfer and Weber–Morris intraparticle diffusion models, Langmuir, Freundlich, Dubinin–Radushkevich, and Temkin isotherm models, and the Gibbs equation. The adsorption isotherm of the larger molecules, RIF and STM, could be explained by the Langmuir isotherm model, in contrast, that of IBU, which is a much smaller molecule, followed the Freundlich isotherm model. The maximum adsorption capacity of RIF, STM, and IBU on chitosan was estimated to be 66.91 mg g−1, 11.00 mg g−1, and 24.21 mg g−1, respectively, which are higher compared to those on a variety of agricultural wastes, suggesting that this biopolymer is a potential practical and economical adsorbent to remove the pharmaceutical compounds from wastewater. The adsorption mechanism of the pharmaceutical compounds on chitosan is proposed based on the vibrational spectroscopic analyses, XRD patterns, and DSC thermograms of the biopolymer before and after adsorption process.