In the present work we investigated the feasibility of chitosan treated Ca-alginate microparticles for delivery of naproxen in lower parts of GIT and evaluated influence of formulation factors on their physicochemical characteristics and drug release profiles. Investigated factors were drug/polymer ratio, chitosan molecular weight, chitosan concentration in hardening medium, and hardening time. Sixteen microparticle formulations were prepared utilizing 24 full factorial design (each factor was varied at two levels). Microparticles size varied between 262.3 ± 14.9 and 358.4 ± 21.7 μm with slightly deformed spherical shape. Low naproxen solubility and rapid reaction of ionotropic gelation resulted in high encapsulation efficiency (> 75.19%). Under conditions mimicking those in the stomach, after two hours, less than 6.18% of naproxen was released. Significant influence of all investigated factors on drug release rate was observed in simulated small intestinal fluid. Furthermore, experimental design analysis revealed that chitosan molecular weight and its concentration had the most pronounced effect on naproxen release. Release data kinetics indicated predominant influence of a pH-dependent relaxation mechanism on drug release from microparticles.