The article presents data on the synthesis and antimicrobial properties of guanidine-containing carboxymethylcellulose derivatives with different physical and chemical characteristics. The regularities of the reaction of nucleophilic substitution of aldehyde groups of modified Na-carboxymethylcellulose (Na-CMC) by guanidine under different conditions are studied. Based on the results obtained, it was found that the limit replacement of reactive electrophilic groups with nucleophilic reagent depends on the pH value of the medium, molar ratio of guanidine and the degree of oxidation of cellulose ester. By varying the reaction conditions and the number of aldehyde groups in the oxidized Na-CMC composition, the azometin derivatives differing in the content of nitrogen-containing fragments in the polymer chain were obtained. Chemical restoration of labile azomethine bonds was performed and water-soluble derivatives containing strong amino-bound guanidine groups were synthesized. The study shows and substantiates the influence of structural indices (degree of substitution, quantitative guanidine content, pKα values and nature of counterion) of macromolecular systems on antibacterial and antifungal properties. The developed approach of synthesis opens prospects for creation of antimicrobial derivatives with regulated physical and chemical characteristics and set biologically active properties.