Chitin-rich organic waste in water creates habitats for microorganisms that can break down chitin into chitosan, a valuable biopolymer used in farming, biotechnology, and environmental management. Environmental and physicochemical process parameters strongly influence the efficiency of microbial chitosan production, which is a sustainable alternative to conventional chemical extraction. This study investigated the occurrence, chitinolytic potential, and chitosan-producing capacity of indigenous microorganisms isolated from freshwater and sediment samples in Minna, Niger State, Nigeria, and optimized production under controlled fermentation conditions. Physicochemical characteristics of water bodies were determined, followed by the isolation and characterization of bacterial and fungal chitinolytic strains. Selected isolates were screened for chitinase activity and subjected to fermentation-based chitosan production. Process optimization was performed using a five-factor central composite design assessing the effects of temperature, pH, glucose concentration, nitrogen source, and incubation time, with response surface methodology applied for model development and interaction analysis. Low dissolved oxygen and moderate temperatures favored chitinolytic genera including Aspergillus, Bacillus, and Fusarium, with Aspergillus niger exhibiting the highest chitosan yield. Incubation time was the most significant factor (p < 0.001), while temperature, pH, and substrate concentration showed strong interaction effects. Maximum chitosan production (0.38 g·L⁻¹) was achieved at 32.5 °C, pH 4.8–5.35, controlled glucose levels, and extended fermentation (48–72 h). These findings highlight inland aquatic ecosystems as valuable reservoirs of chitinolytic microorganisms and provide an optimized, environmentally benign framework for scalable microbial chitosan production.