The processing of Mollusca for food consumption generates a large amount of by-products; for instance, shells, which may contaminate and deposit in the marine coastal environment. Therefore, additional processing is needed to reduce and transform shells into valuable materials, such as chitosan or another derivate product. This study aimed to isolate and characterize the chitosan from Solen vagina (known as lorjuk shells in Indonesian) and to determine the application of chitosan. This is to be compared with Solen vagina shell powder that commonly functions as bio-sorbent of water pollutants Cu2+, Cd2+, and Pb2+. The isolated chitosan was characterized based on its physicochemical properties, namely purity as tested by using X-ray fluorescence (XRF), and functional group as confirmed by Fourier transform infrared (FTIR). In addition, bio-absorbent ability was evaluated through a column method, where the chitosan products are used and compared with Solen vagina shell powders. In this study, the chitosan isolated from Solen vagina shells yielded 15.92 ± 1.78% and showed a high deacetylation degree (DD) by 85.00 ± 3.98%. FTIR and physicochemical properties analysis confirmed that the isolated chitosan is of good quality, as standardized by industry regulator; thus, it could be used as food product and bio-absorbent material. Moreover, the bio-absorbent ability of chitosan demonstrated a similar value with S. vagina shell powders, which can absorb more than 92% of heavy metals around second elution. In conclusion, the S. vagina shell powder and the isolated chitosan have the potential as natural bio-absorbent to reduce the heavy metal contents in industrial wastewater.