Charge transfer in semiconductor heterojunctions is largely governed by the offset in the energy levels of the constituent materials. Unfortunately, literature values for such energy level offsets vary widely and are usually based on energy levels of the individual materials rather than of actual heterojunctions. Here we present a new method to determine absolute energy levels and energy level offsets in situ for films containing CdSe and PbSe quantum dots. Using spectroelectrochemistry, we find a type I offset at the CdSe-PbSe heterojunction. Whereas the energy level offset follows the expected size-dependent trend, the absolute positions of the 1Se level in the individual CdSe or PbSe quantum dots does not. This level varies by more than 0.5 eV, depending on film composition and surface defect concentration. Rather than extrapolating energy level offsets from measurements on pure CdSe or PbSe quantum-dot films, we suggest measuring energy level offsets in heterojunctions in situ.