Flow effects on the thermal loading in different optofluidic systems (optical trap and various microfluidic channels) have been systematically explored by using dye-based ratiometric luminescence thermometry. Thermal images obtained by fluorescence microscopy demonstrate that the flow rate plays a key role in determining both the magnitude of the laser-induced temperature increment and its spatial distribution. Numerical simulations were performed in the case of the optical trap. A good agreement between the experimental results and those predicted by mathematical modelling was observed. It has also been found that the dynamics of thermal loading is strongly influenced by the presence of fluid flow.