In this paper, the energy transfer phenomena of a secondary facultative lagoon and its relationship with environmental conditions such as wind and solar radiation were studied. To this end, a three-dimensional computational fluid dynamics model was constructed within a conventional facultative lagoon located in the municipality of Ginebra-Valle del Cauca, Colombia. The model included the transport of suspended solids from inlet to outlet, the penetration of incident solar radiation into the body of water, surface wind, the transfer of heat through lateral walls and the temperature profiles of the wastewater. The model was validated using tracer studies and experimental temperature data. This demonstrated that simulated data of temperature and solar radiation penetration have an acceptable degree of consistency compared with the experimental data. The model demonstrated that temperature profiles were significantly affected by the wind at 0.45 m and 1.40 m depth, while no effect on the surface was obtained.