Chitosan and modified chitosan have been proved for numerous biological and water treatment applications including as strong antimicrobial agents. In this work the main target of functionalization of chitosan with amine group protection. Chemical modification of chitosan serves as a great opportunity to design and develop broad spectrum antibacterial agents. Chitosan derivatives were synthesised and tested for antimicrobial action against gram positive and gram-negative bacteria as well as for Fungi. The result of FTIR and NMR analysis disclosed successfully protection of the Amine group and covalent attachment of different functional groups with polymer backbone. The chemically modified polymers were found active against both bacteria and fungi with MIC value (MIC = 100-250 μg/mL). Moreover, the derivatives were shown higher activity with lower MIC values as compare to reported Chitosan derivatives with different organic synthetic protocol. Chemically modified chitosan was evaluated as an adsorbent for the removal of copper (II) and nickel (II) from water. Experimental data of Atomic Absorption spectroscopy shows higher affinity towards Nickel (II) as compared to Copper (II).