The microbial breakdown of chitosan, a fishery waste-based material, and its derivative cross-linked chitosans, in both non-contaminated and contaminated conditions was investigated in a laboratory incubation study. Biodegradation of chitosan and cross-linked chitosans was affected by the presence of heavy metals. Zn was more pronounced in inhibiting microbial activity than Cu and Pb. It was estimated that a longer period is required to complete the breakdown of the cross-linked chitosans (up to approximately 100 years) than unmodified chitosan (up to approximately 10 years). The influence of biodegradation on the bioavailable fraction of heavy metals was studied concurrently with the biodegradation trial. It was found that the binding behaviour of chitosan for heavy metals was not affected by the biodegradation process.