The effects of the underwater light field on heat-budget calculations for shallow waters are developed and applied for the region of Bahamas. Most of the general circulation models use a simplified heat budget scheme based on Jerlov water types, and do not account for optical bottom effects. by optical bottom effect, we mean the bottom absorption and reflection of the short-wave radiation, which in turn affects the thermal stratification and heat exchange with the atmosphere. In this paper, this optical bottom effect is added to a 3D turbulence model (a 1D model called GOTM is coupled to a 3D model called POM) and the evolution of the temperature structure studied. We call the coupled model 3DGOTM. This optical bottom effect is found to be important in the areas with clear water, shallow depths and small solar zenith angle. On the basis of the coastal meteorological measurements from Andros Island, we have used this three-dimensional turbulence closure model (3DGOTM) to show the influence of bottom reflection and absorption on the sea surface temperature field. The final temperature of the developed water column depends on water depth and bottom albedo. Effects of varying the bottom albedo were studied by comparing results for coral sand and sea grass bottoms. This has an appreciable contribution to the heat budget and salt budget of the shallow waters in these coastal regions. The salinities of the shallow regions near Andros Island have been found to reach as high as 46 psu by summer. In addition to the thermohaline plumes generated by these bottom effects, this warming process has an impact on the moisture feedbacks into the atmosphere due to evaporation.