E. coli YqhD exhibits aldehyde reductase and alcohol dehydrogenase activity with a broad substrate range. It has applications in the production of valuable biorenewable fuels and chemicals, such as isobutanol and 1,3-propanediol. Hence, this enzyme is an ideal candidate for protein engineering studies. In this work, we shed light on the change of conformational dynamics of YqhD in the presence of different substrates. Molecular dynamics simulations of YqhD were performed in pure water and near experimental concentrations of alcohols and aldehydes as substrates. The study aims to enhance the knowledge about the effect of substrate-enzyme interactions on the overall dynamics of the enzyme, and how these dynamics influence substrate accessibility to the active site. The outcome of the study will enhance our basic understanding of the relationships among structure, dynamics and function within this class of enzyme. The results have possible application to guide the rational design of YqhD to enhance substrate specificity and facilitate transport to the active site.