Well killing operation remains an important technological stage before well workover or servicing, during which filtrate penetrates the bottomhole area of the formation. The impact of process fluids and their filtrate on rock has a significant influence on permeability and porosity of carbonate reservoirs, which decrease due to fines migration. There are few known scientific studies of the interaction of killing fluid filtrate with carbonate rock and fines migration. In our experiments, an aqueous phase was used which is the basis for well killing in pure form, for the preparation of blocking agents and is used in reservoir pressure maintenance system. Core samples taken from the pay of the reservoir were used to simulate the well killing process with generation of reservoir thermobaric conditions. Killing fluid filtrate was kept for seven days, which characterizes the average workover time at flowing wells in the fields of the Perm Territory. Using micro-X-ray tomography and scanning electron microscope, images were obtained before and after the experiment, which allowed confirming a decrease in total number of voids due to fines migration and, as a consequence, a decreasing permeability of samples. Measurement of pH and fines concentration in the aqueous phase was performed before and after the experiment and pointed to mineral reactions occurring as a result of rock dissolution. The results of experiments made it possible to record a decrease in permeability of carbonate samples by an average of 50 % due to clogging of void space and migration of fines (clayey and non-clayey).