Water hyacinth ( Eichhornia crassipes C. Mart.) and Brazilian elodea ( Egeria densa Planch.) are non-native aquatic macrophytes in Lake Fuquene (Colombia) that cover more than 70% of the water body. As a control technique, the macrophytes are harvested by mechanical means and they can be exploited by composting using native beneficial microorganisms to accelerate the process and also to improve the final product quality. In this research, from five composting treatments with these macrophytes, 159 microbial strains were isolated and by testing antagonism, 16 bacteria, 24 fungi and 21 actinomycetes were chosen to produce three inoculants by submerged fermentation. The microbial inoculants were added in a second composting, using the best first composting treatments. By inoculating the microorganisms, the degradation process was accelerated between 23 to 35%. The assay conducted on radish seedlings ( Raphanus sativus L.), using as treatments, compost with microbial inoculants (T2i, T4i and T5i) and chicken manure at 33% mixed with soil (control), showed no significant differences ( P <0.05) with respect to growth, bulb formation and bulb weight. However, compost inoculated treatments showed significant increases in leaf nutrients compared with chicken manure. The use of microorganisms showed to be an efficient technique for the aquatic invasive plant management of Lake Fuquene using composting to obtain a very high quality agricultural product with good nutritional and biological quality. Key words: Water hyacinth, Brazilian elodea, Lake Fuquene, Endogenous microbial inoculants, composting.