Microplastic pollution from polyethylene (PE) and polystyrene (PS) remains difficult to remediate using conventional metal-based coagulants due to sludge generation and environmental risks. This study develops and evaluates a fully bio-based, Fe/Al-free coagulation system using chitosan enhanced with calcium ions (Ca²⁺) and tannic acid. Coagulation experiments were performed under controlled variations of pH, chitosan dosage, slow mixing duration, and coagulant aids. Removal performance was quantified gravimetrically, while mechanisms were elucidated through zeta potential, ATR-FTIR, and SEM analyses. Chitosan showed markedly higher coagulation efficiency at near-neutral pH, achieving 18.53% removal for PE and 47.66% for PS. The incorporation of Ca²⁺ or tannic acid further improved removal to 27.13% and 65.03%, respectively. Mechanistic characterization demonstrated that charge neutralization, ionic bridging, hydrogen bonding, hydrophobic interactions, and π–π stacking collectively govern microplastic aggregation. Ca²⁺ promoted electrical double-layer compression and enhanced floc compactness, whereas tannic acid strengthened adsorption through phenolic–amine interactions and aromatic affinity with PS. An Artificial Neural Network (ANN) model incorporating six operational parameters successfully captured the nonlinear relationships influencing removal efficiency, showing good predictive performance within the experimental domain and providing insights into parameter contributions. Overall, the findings highlight the potential of chitosan-based systems as sustainable, metal-free alternatives for microplastic mitigation. The synergistic role of Ca²⁺ and tannic acid offers a pathway toward scalable, environmentally safe coagulation technologies for water treatment applications.