Transition metal multilayers are prime candidates for high reflectivity soft x-ray multilayer mirrors. In particular, Cr/Sc multilayers in the amorphous state have proven to give the highest reflectivity in the water window. We have investigated the influence of impurities N and O as residual gas elements on the growth, structure, and optical performance of Cr/Sc multilayers deposited in high vacuum conditions by a dual cathode direct current magnetron sputter deposition. Multilayer structures with the modulation periods in the range of 0.9–4.5 nm and Cr layer to bilayer thickness ratios in the range of 0.17–0.83 were deposited with an intentionally raised base pressure (pB), ranging from 2 × 10−7 to 2 × 10−5 Torr. Compositional depth profiles were obtained by elastic recoil detection analysis and Rutherford backscattering spectroscopy, while the structural investigations of the multilayers were carried out using hard x-ray reflectivity and transmission electron microscopy. By investigating stacked multilayers, i.e., several multilayers with different designs of the modulation periods, stacked on top of each other in the samples, we have been able to conclude that both N and O are incorporated preferentially in the interior of the Sc layers. At pB ≤ 2 × 10−6 Torr, typically <3 at.% of N and <1.5 at.% of O was found, which did not influence the amorphous nanostructure of the layers. Multilayers deposited with a high pB ∼2 × 10−5 Torr, a N content as high as ∼37 at.% was measured by elastic recoil detection analysis. These multilayers mainly consist of understoichiometric face-centered cubic CrNx/ScNy nanocrystalline layers, which could be grown as thin at 0.3 nm and is explained by a stabilizing effect on the ScNy layers during growth. It is also shown that by adding a background pressure of as little as 5 × 10−6 Torr of pure N2 the soft x-ray reflectivity (λ = 3.11 nm) can be enhanced by more than 100% by N incorporation into the multilayer structures, whereas pure O2 at the same background pressure had no effect.