X‐ray standing wave (XSW) field generated under Bragg reflection condition in a periodic Mo/Si multilayer structure has been used to determine the concentration and location of various trace element contaminants embedded in different layers of that multilayer structure. We have used intense synchrotron X rays for XSW analysis. It is observed that various trace element impurities such as Cr, Fe, Ni and W get embedded unintentionally in the multilayer structure during the deposition process. Consequences of such impurity incorporation on the optical properties of the multilayer structure are discussed in hard and soft X‐ray regions. Present measurements are important in order to optimize the deposition methods on one hand and to better correlate the measured optical properties of a multilayer structure with theoretical models on the other. Copyright © 2010 John Wiley & Sons, Ltd.