In recent years, the invasive pleco fish has emerged as a global concern due to its adverse effects on ecosystems and economic activities, particularly in various water bodies in Mexico. This study introduces an innovative solution, employing microwave-assisted hydrothermal carbonization (MHTC) to synthesize hydrochar from pleco fish biomass. The research aimed to optimize synthesis conditions to enhance hydrochar yield, calorific value, and adsorption capacities for fluoride and cadmium in water. MHTC, characterized by low energy consumption, high reaction rates, and a simple design, was employed as a thermochemical process for hydrochar production. Key findings revealed that through response surface analysis, the study identified the optimal synthesis conditions for hydrochar production, maximizing yield and adsorption capacities while minimizing energy consumption. Physicochemical characterization demonstrated that hydrochars derived from pleco fish biomass exhibited mesoporous structures with fragmented surfaces, resembling hydroxyapatite, a major component of bone. Hydrochars derived from pleco fish biomass exhibited promising adsorption capacities for fluoride and cadmium in water, with hydrochar from Exp. 1 (90 min, 160 °C) showing the highest adsorption capacity for fluoride (4.16 mg/g), while Exp. 5 (90 min, 180 °C) demonstrated superior adsorption capacity for cadmium (98.5 mg/g). Furthermore, the utilization of pleco fish biomass for hydrochar production not only offers an eco-friendly disposal method for invasive species but also addresses fluoride and cadmium contamination issues, contributing to sustainable waste management and water treatment solutions. The resulting hydrochar, rich in solid fuel content with low pollutant emissions, presents a promising approach for waste management and carbon sequestration. Moreover, the optimized synthesis conditions pave the way for sustainable applications in energy production, addressing critical environmental and public health concerns. This research provides valuable insights into the potential of microwave-assisted hydrothermal carbonization for transforming invasive species into valuable resources, thereby mitigating environmental challenges and promoting sustainable development.