As the scaling of electronic components continues, local heating will have an increasing influence on the stability and performance of nanoscale electronic devices. In particular, the low heat capacity of molecular junctions means that it will be essential to understand local heating and heat conduction in these junctions. Here we report a method for directly monitoring the effective temperature of current-carrying junctions with surface enhanced Raman spectroscopy (SERS) that involves measuring both the Stokes and anti-Stokes components of the Raman scattering. All the Raman-active modes in our system show similar heating as a function of bias at room temperature, which suggests fast vibrational relaxation processes inside the junctions. These results demonstrate the power of direct spectroscopic probing of heating and cooling processes in nanostructures.