Successful enzyme catalysis depends on many noncovalent interactions between the enzyme, cofactors, and substrate that poise the system to access a productive transition state. Motions on a variety of timescales contribute to this, but some controversy exists surrounding the role of ultrafast dynamics on catalysis. Site-specific 2D IR spectroscopy using probes of vibrational dynamics provides the opportunity to explore ultrafast motions in an enzyme active site owing to the technique’s spatial and temporal resolution. In this work, a series of aryl-azide vibrational labels were assessed using a variety of 2D IR techniques for their sensitivity to solvent and energy transfer processes, and their ability to be adapted to experiments in biomacromolecules. One of these labels, 4-azido-N-phenylmaleimide, is a substrate analog for the promiscuous ene-reductase from Pyrococcus horikoshii (PhENR). The label was covalently attached in two orientations in the enzyme active site, occupying the same position as native substrates based on X-ray crystallography and molecular dynamics simulations. FTIR and 2D IR spectroscopy were used to identify close-lying conformational states based on the strong anharmonic coupling of the label, revealing that the active site itself modulates the probe’s internal vibrational coupling. More commonly used analogous aryl-nitrile labels, however, were not sensitive to such small structural and lineshape changes. This demonstrates the importance of thoughtful label design to maximize the amount of information that can be gleaned from 2D IR studies. Using the methods herein—both spectroscopic and biochemical—provides a strategy for probing ultrafast motions that could possibly be catalytically relevant.