A mechanistic model was developed to describe the thermal behavior of an indoor raceway system with an inflated double polyethylene cover. The model describes the heat balances of the two covers, the inside air, the water in the raceway and the soil beneath the raceway. On-site measurements were made with an experimental system at the Waddell Mariculture Center in South Carolina. The collected data were used to calibrate the model. Comparison of the predictions with observations showed that the average absolute errors of air temperature and water temperature were 1.4 and 0.5°C, respectively and was 8% for the relative humidity. The accuracies are regarded as sufficient for the model to be useful for more general application. Model simulations were used to investigate the effects of the greenhouse on the air and water temperatures, to examine the heat fluxes and to calculate the heat consumption and costs at four different climatic locations. The results suggest that under the mild weather conditions in January near Charleston, SC where the daily mean temperature is 7.6°C and solar radiation is 121Wm−2, the inside air temperature increases by 5.6°C and water temperature increases by 9.7°C on average for the system with the 0.85m deep raceway covering 70% of the greenhouse floor. An examination of the heat fluxes suggests that thermal radiation is a major mechanism of heat loss for the greenhouse covers and the water surface. Convection from the water surface is also a significant mechanism for latent and sensible heat loss from the raceway. Reducing these heat flows will help conserve and utilize energy. The yearly heating requirements to keep the water temperature at 28°C for the experimental system were estimated to be 870, 520, 274 and 221 kWh per square meter of raceway for Syracuse, NY, Roanoke, VA, Charleston, SC and Baton Rouge, LA, respectively. The model was deemed to be a useful tool for exploring the performance of greenhouse raceway systems under different scenarios, such as different cover materials, sizes and climates.