Harmful algal blooms (HABs) are natural phenomenon that threatens public health, tourism, fisheries and ecosystems. Silica in its natural form is unable to mitigate HABs effectively and frequently modified with chitosan. In this study, the influence of crosslinking and swelling properties of rice husk ash silica/chitosan film reinforced with (3-glycidyloxypropyl) trimethoxysilane (GPTEOS) and glycerol (Gly) in capturing HABs cell, Alexandrium minutum was thoroughly investigated. The XRD analysis indicated that crosslinking had caused part of the chitosan’s crystalline network to become amorphous. The FTIR analysis showed that the chitosan, silica, glycerol and GPTEOS were crosslinked via a condensation reaction. The crosslinking was higher in the film containing GPTEOS (CHT/SiO2/GPTEOS) due to the condensation reaction between the GPTEOS epoxy group and the amine of chitosan in addition to the condensation of silanol and hydroxyl group of chitosan. As a result, the swelling of CHT/SiO2/GPTEOS was lower compared to Gly-containing film (CHT/SiO2/Gly). The RE value was 26.57 ± 10.81% using CHT/SiO2/Gly and 50.06 ± 11.90% using CHT/SiO2/GPTEOS. Based on the swelling and the RE trends, it is concluded that the initially trapped algae could have been released back into the environment when the films swelled. This study shows that crosslinking is important trapping the algae. The SEM and digital microscopic images of the used films revealed the presence of algae cells on the surface of the films. The films could be easily separated from the algae culture without sedimentation. The films also showed good biodegradability as all the films were fully degraded within 30 days of burial.