Scale formation and deposition in the subsurface and surface facilities have been recognized as a major cause of flow assurance issues in the oil and gas industry. Sulfate-based scales such as sulfates of calcium (anhydrite and gypsum) and barium (barite) are some of the commonly encountered scales during hydrocarbon production operations. Oilfield scales are a well-known flow assurance problem, which occurs mainly due to the mixing of incompatible brines. Researchers have largely focused on the rocks’ petrophysical property modifications (permeability and porosity damage) caused by scale precipitation and deposition. Little or no attention has been paid to their influence on the surface charge and wettability of calcite minerals. Thus, this study investigates the effect of anhydrite and barite scales’ presence on the calcite mineral surface charge and their propensity to alter the wetting state of calcite minerals. This was achieved vis-à-vis zeta-potential (ζ-potential) measurement. Furthermore, two modes of the scale control (slug and continuous injections) using ethylenediaminetetraacetic acid (EDTA) were examined to determine the optimal control strategy as well as the optimal inhibitor dosage. Results showed that the presence of anhydrite and barite scales in a calcite reservoir affects the colloidal stability of the system, thus posing a threat of precipitation, which would result in permeability and porosity damage. Also, the calcite mineral surface charge is affected by the presence of calcium and barium sulfate scales; however, the magnitude of change in the surface charge via ζ-potential measurement is insignificant to cause wettability alteration by the mineral scales. Slug and continuous injections of EDTA were implemented, with the optimal scale control strategy being the continuous injection of EDTA solutions. The optimal dosage of EDTA for anhydrite scale control is 5 and 1 wt % for the formation water and seawater environments, respectively. In the case of barite, in both environments, an EDTA dosage of 1 wt % suffices. Findings from this study not only further the understanding of the scale effects on calcite mineral systems but also provide critical insights into the potential of scale formation and their mechanisms of interactions for better injection planning and the development of a scale control strategy.