The presence of impurities in the molecular crystals of organic semiconductors is a key limiting factor for the performance of related electronic devices. For this reason, the atomic-scale details of impurity incorporation are important elements for modeling and optimization of organic electronic systems. In this article, we use first-principles density-functional theory calculations to describe the vibrational spectrum of typical impurity culprits in the prototype organic semiconductor pentacene. First, we validate the computational approach by comparing results on vibrational modes of impurity-free pentacene with available theoretical and experimental data. We then analyze the effect of oxygen, water, and hydrogen impurities on the modes of pentacene crystals. The results identify distinct impurity-related features which can help understand the evolution of impurities in pentacene samples.