Technical Abstract: A low cost system was deployed above a swine waste lagoon to obtain estimates of Bowen ratios and characterize lagoon temperatures. The system consisted of humidity and temperature sensors and anemometers deployed above the lagoon, water temperature sensors, and a meteorological station located by the lagoon. To evaluate the system, data was analyzed from the 25th through 28th June, 2007. Bowen ratios showed diurnal behavior near the lagoon surface characterized by negative values during day and positive ones at night. Latent (evaporation) and sensible heat fluxes were towards the atmosphere and the lagoon, respectively for most of the day. A diurnal cycle in atmospheric and lagoon temperatures was also observed. Furthermore, wind speeds above the lagoon were highest in the afternoon. These variations were linked to lagoon temperature stratifications which became more pronounced as wind speeds increased. Temperature stratification at the lagoon indicated increased heat exchange at the lagoon’s interface with the atmosphere. During the night, the stratification disappeared and temperatures in the water column were almost identical down to about 60 cm. This behavior is similar to that observed in other shallow water bodies that are fetch-limited. Lagoon heating was driven by the diurnal cycle of solar radiation and net radiation. This suggests that Bowen ratios had an inverse relationship with lagoon heating and its thermal stratification. This also indicates that there was an increase in latent heat flux and evaporation during the daytime. These results are important for characterizing the thermal behavior of the lagoon leading to a better representation of processes responsible for emissions.