In this study, composting as an alternative approach for managing mercury-contaminated biomass in water bodies affected by gold mining in the Choco department was evaluated. A single-factor experiment with three treatments containing varying amounts of Eleocharis interstincta biomass sourced from mercury-contaminated sites was designed. During the composting process, physicochemical parameters were monitored such as temperature, pH, and electrical conductivity, while analyzing the behavior of mercury through mass balance assessments. Additionally, we determined the bioavailability of mercury in the final compost and characterized the physicochemical parameters of each compost sample. The mercury mass balance indicated a decrease in the total mercury content in the initial biomass over the composting period of 170 days. However, the total mercury concentration in the final compost increased due to the transformation and subsequent reduction of the original biomass. Mercury speciation analysis revealed that mercury was predominantly associated with the less bioavailable fractions (F4 and F5), suggesting its stabilization and low availability to biota. Therefore, the final compost has the potential to restore degraded soils by improving moisture retention, porosity, and soil fertility, thereby promoting plant growth. However, it does not fully meet the national and international technical standards for solid organic fertilizers or compost.