Throughout the life of a well, its cement sheath may fail through the development of micro-annuli along the boundaries of its structure. The occurrence and attributes of these annuli may be influenced by the processes of drilling and completions, in addition to the in-situ conditions. This paper presents a staged finite element modeling approach to determine the effects that variations in the elastic properties between cement grades and rock lithologies, as well as encountered stress regimes, have upon the properties of micro-annuli formation within water injection wells. The model set-up is achieved through an initiation of the chosen stress field, implementation of borehole fluid pressures, and temperature decrease for the water injection phase. The effects of the difference in elastic parameters between the cement grade and formation rock on micro-annulus formation are achieved by evaluating multiple model combinations of both components. Similarly, the influences of the stress regime on the micro-annuli are determined by implementing differing intensities of stress contrast into the model, as well as considering depth variations. The research results indicate that the aperture magnitude of the developed micro-annuli, as well as its timing of initiation, depend upon both the Young’s moduli contrast between cement and formation materials and the depth considered. Additionally, the orientation of the aperture appears to rely on the stress regime in which the wellbore is enveloped. These observations could be utilized to better prevent wellbore leakage by selecting cement-formation pairs that possess a lower chance of micro-annuli formation and by being aware of the asymmetric and aperture widening effects of different stress regimes on this pervasive mode of failure.