The NADPH-dependent alcohol dehydrogenase (YqhD) from E. coli is a promiscuous enzyme with low substrate specificity. YqhD exhibits aldehyde reductase and alcohol dehydrogenase activity with a broad substrate range and produces biofuels and valuable chemicals. The industrial applicability of the enzyme makes it an ideal candidate for protein engineering studies with the available structure and kinetic information. Herein, we shed light on the substrate promiscuity of YqhD using molecular dynamics (MD) simulations. The MD simulations of YqhD were performed in pure water and at experimental concentrations of substrates, such as isobutaraldehyde and propanaldehyde. The study aims to enhance the knowledge about substrate dynamics in the active site and around the protein, and their relationship to protein structure, function and dynamics. The outcome of the study will enhance our basic understanding of this class of enzyme, with the possible application to guide the rational design of YqhD or related alcohol dehydrogenases to facilitate substrate transport to the active site for enhanced function.