Monitoring the interactions between electronic and vibrational degrees of freedom in molecules is critical to our understanding of their structural dynamics. This is typically hampered by the lack of spectroscopic probes able to detect different energy scales with high temporal and frequency resolution. Coherent Raman spectroscopy can combine the capabilities of multidimensional spectroscopy with structural sensitivity at ultrafast timescales. Here, we develop a three-color-based 2D impulsive stimulated Raman technique that can selectively probe vibrational mode couplings between different active sites in molecules by taking advantage of resonance Raman enhancement. Three temporally delayed pulses generate nuclear wave packets whose evolution reports on the underlying potential energy surface, which we decipher using a diagrammatic approach enabling us to assign the origin of the spectroscopic signatures. We benchmark the method by revealing vibronic couplings in the ultrafast dynamics following photoexcitation of the green fluorescent protein.