The potential application of Water Hyacinth (Eichhornia crassipes) in organic matter degradation, sedimentation, nutrient and heavy metal absorption and sulfur reduction in the Muña Reservoir has been tested in experimental lagoons. The lagoons were operated at hydraulic retention times (HRT) of 6, 9 and 15 days. One lagoon was covered with Water Hyacinth, which is naturally growing in the Muña Reservoir, while another lagoon was operated as a conventional oxidation pond. The Water Hyacinth lagoon had better removal efficiencies for almost all parameters measured: BOD5, total suspended solids, COD, nitrogen, phosphorus and heavy metals. The oxidation lagoon was facultative for HRT of 9 and 15 days, and anoxic when operated at 6 days HRT. At HRT of 15 days the water quality in the effluent of the covered lagoon corresponded to 12 mg/l of BOD, 6 mg/l of suspended solids and 0.8 mg/l of hydrogen sulfide. Hydrogen sulfide levels in the Muña reservoir can be substantially reduced at HRT higher than 15 days in both lagoons. The uncovered lagoon had better hydrogen sulfide removal during the day but presents high levels at night. If the hydraulic retention time in the Muña reservoir is increased, the water quality of the Bogota river can be substantially improved for all the HRTs tested in the pilot units. HRT seems to give a better prediction of overall effluent water quality than surface loading. More research is needed in order to define the optimum water hyacinth density in the Muña reservoir to determine its influence on the water quality of the effluent. The influence is expected to be negative due to an internal increase of BOD, solids, nutrients and metals loads due to plant decay.