Polycyclic aromatic hydrocarbons (PAHs) are complex molecules produced by the thermal decomposition of organic matter in anthropogenic activities. Novel composites with enhanced physicochemical properties aim to overcome limitations such as adsorption capacity, affinity, and stability for PAHs adsorption. Composites based on chitosan are promising due to the good biocompatibility and adsorption properties. This study focuses on the facile preparation of chitosan beads modified with iron oxide (FeO) and titanium dioxide (TiO) nanoparticles via ionic cross-linking (Ch-FeO/TiO). FeO and TiO were synthesized performing co-precipitation and green chemistry methods, respectively. The characterization evidenced the formation of Ch-FeO/TiO with good crystallinity, excellent thermal stability, and superparamagnetic response, attributed to the presence of FeO and TiO nanoparticles. High thermal stability up to 270 °C was related to the cross-linked chitosan network. The enhanced adsorption mechanism of Ch-FeO/TiO was determined by removing naphthalene from water and seawater samples. The Ch-FeO/TiO showed a higher adsorption capacity of 33.1 mg/g compared to 29.8 mg/g of the unmodified chitosan (un-Ch) beads. This is due to the higher functional surface area of 27.13 m/g, compared to that of 0.708 m/g for un-Ch. We found a rapid adsorption rate of 240 min and the maximum adsorption capacity of 149.3 mg/g for Ch-FeO/TiO. A large number of actives sites allows for increasing the naphthalene molecules interaction. Adsorption in seawater samples from Cartagena Bay (Colombia) exhibits an outstanding efficiency of up to 90%. These results suggest a promising, cheap, and environmentally friendly composite for remediation of water sources contaminated with complex compounds.