The differential interferometric synthetic aperture radar (DInSAR) method is based on phase variation between the complex value of pixels of timely separated scenes in interferometric SAR pairs. This phase variation has five components: surface topography, curvature of planet’s surface, terrain displacement, volume scatterers, and atmospheric propagation effects. The terrain displacement is the main product of the DInSAR method, while the last two effects are unpredictable and bring inaccuracy into the terrain displacement measurements. In this work, the propagation conditions in the troposphere and ionosphere were studied during two DInSAR measurements examining the Zagreb 22 March 2020 earthquake, with terrain raising of up to +3 cm at the epicenter. For the troposphere, the vertical profile of the modified refraction index, which incorporates local curvature change with height, was reconstructed using aerological balloon probing data. Ionospheric conditions were determined based on total electron content (TEC) calculated from the Croatian positioning system (CROPOS) and global navigation satellite system (GNSS) reference stations’ measurements. One of the DInSAR measurements was conducted in unfavorable tropospheric refractive conditions, which resulted in an overall bias of −2 cm. The variability of propagation conditions indicates the need for examining the atmospheric propagation effects when calculating terrain displacements using the DInSAR method. The results of DInSAR indicate slight displacements, comparable with the amplitude of atmospheric variations, and should therefore be approached with caution.