Thermal analysis with comprehensive treatment of conjugate heat transfer is performed in this study for discrete flush-mounted heat sources in a horizontal channel cooled by air. The numerical model accounts for mixed convection, radiative exchange and two-dimensional conduction in the substrate. The model is first used to simulate available experimental work to demonstrate its accuracy and practical utility. A parametric study is then undertaken to assess the effects of Reynolds number, surface emissivity of walls and heat sources, as well as thickness and thermal conductivity of substrate, on flow field and heat transfer characteristics. It is shown that due to radiative heat transfer, the wall temperatures are brought closer, and the trend of temperature variation along the top wall is significantly altered. Such effects are more pronounced for higher surface emissivity and/or lower Reynolds numbers. The influence of substrate conductivity and thickness is related in that a large value of either substrate conductivity or thickness facilitates redistribution of heat and tends to yield a uniform temperature field in the substrate. For highly conductive or thick substrate, the “hot spot” cools down and may occur in upstream sources. Radiation loss to the ambient increases with substrate conductivity and thickness due to the elevated temperature near the openings, yet the total heat transfer over the bottom surface by convection and radiation remains essentially unaltered.