The magnetic mesoporous hydrogel-based nanoadsornet was prepared by adding the ex situ prepared Fe3O4magnetic nanoparticles (MNPs) and bentonite clay into the three-dimentional (3D) cross-linked pectin hydrogel substrate for the adsorption of organophosphorus chlorpyrifos (CPF) pesticide and crystal violet (CV) organic dye. Different analytical methods were utilized to confirm the structural features. Based on the obtained data, the zeta potential of the nanoadsorbent in deionized water with a pH of 7 was − 34.1 mV, and the surface area was measured to be 68.90 m2/g. The prepared hydrogel nanoadsorbent novelty owes to possessing a reactive functional group containing a heteroatom, a porous and cross-linked structure that aids convenient contaminants molecules diffusion and interactions between the nanoadsorbent and contaminants, viz., CPF and CV. The main driving forces in the adsorption by the Pectin hydrogel@Fe3O4-bentonite adsorbent are electrostatic and hydrogen-bond interactions, which resulted in a great adsorption capacity. To determine optimum adsorption conditions, effective factors on the adsorption capacity of the CV and CPF, including solution pH, adsorbent dosage, contact time, and initial concentration of pollutants, have been experimentally investigated. Thus, in optimum conditions, i.e., contact time (20 and 15 min), pH 7 and 8, adsorbent dosage (0.005 g), initial concentration (50 mg/L), T (298 K) for CPF and CV, respectively, the CPF and CV adsorption capacity were 833.333 mg/g and 909.091 mg/g. The prepared pectin hydrogel@Fe3O4-bentonite magnetic nanoadsorbent presented high porosity, enhanced surface area, and numerous reactive sites and was prepared using inexpensive and available materials. Moreover, the Freundlich isotherm has described the adsorption procedure, and the pseudo-second-order model explained the adsorption kinetics. The prepared novel nanoadsorbent was magnetically isolated and reused for three successive adsorption–desorption runs without a specific reduction in the adsorption efficiency. Therefore, the pectin hydrogel@Fe3O4-bentonite magnetic nanoadsorbent is a promising adsorption system for eliminating organophosphorus pesticides and organic dyes due to its remarkable adsorption capacity amounts.