Aerogels have emerged as appealing materials for various applications due to their unique features, such as low density, high porosity, high surface area, and low thermal conductivity. Aiming to bring the advantages of these materials to the environmental field, this study focuses on synthesizing magnetic silica aerogel-based films suitable for water decontamination. In this respect, a novel microfluidic platform was created to obtain core-shell iron oxide nanoparticles that were further incorporated into gel-forming precursor solutions. Afterward, dip-coating deposition was utilized to create thin layers of silica-based gels, which were further processed by 15-hour gelation time, solvent transfer, and further CO2 desiccation. A series of physicochemical analyses (XRD, HR-MS FT-ICR, FT-IR, TEM, SEM, and EDS) were performed to characterize the final films and intermediate products. The proposed advanced imaging experimental model for film homogeneity and adsorption characteristics confirmed uniform aerogel film deposition, nanostructured surface, and ability to remove pesticides from contaminated water samples. Based on thorough investigations, it was concluded that the fabricated magnetic aerogel-based thin films are promising candidates for water decontamination and novel solid-phase extraction sample preparation.