Chitosan, which is a naturally derived polysaccharide obtained through the deacetylation of chitin, has emerged as one of the most versatile and extensively studied biopolymers for biological applications. Its widespread use is due to its intrinsic bioactive properties, including biocompatibility, biodegradability, and notable bioactivities such as antimicrobial, antioxidant, and mucoadhesive effects. While the antimicrobial activity of chitosan has been extensively evaluated against a wide range of microorganisms, including bacteria, yeasts and fungi from various sources, its specific effects on fish pathogens remain less explored. To address this knowledge gap, the present case study analyses the antimicrobial potential of chitosan formulated into various biomaterial forms, including hydrogels, films, and nanoparticles. We make a comprehensive analysis of the physicochemical properties of some of the most used chitosan-based materials, along with a targeted evaluation of their antimicrobial efficacy against fish-related microbial strains, aiming to advance their application in aquaculture and the management of ecological fish health. The controlled application of chitosan in natural aquatic systems such as Prut River Basin requires an adaptative approach which should take into account several environmental parameters. A case study on the impact of temperature variations and chemical stress on the immune system of fish species from Prut river basin has been performed, highlighting the necessity of finding solutions for improving the fish immunity system. Future research should focus on assessing the ecological impact of different chitosan materials and developing practical application strategies based on the local conditions.