Micro-XRCT data sets (projection and reconstructed images) of an in-situ experiment with an X-ray transparent flow cell. As a porous medium, a 3 mm cylindrical sandstone core from the County of Bentheim was investigated. The conceptual design of the cell was presented in Fusseis et al. (2014) and offers the possibility to apply a confining and backpressure, and to inject a pore fluid under X-ray radiation. Two scans were performed. The first scan was performed on the dry sample. The second scan was performed after the sample was saturated with 3M KI solution (3 mol potassium iodide per liter distilled water) with a constant flow of 100 µl/s against a backpressure of 0.28 MPa. To prevent hydrogen formation due to the X-rays, a flow of 0.5 µl/s was maintained against a backpressure of 0.28 MPa during the entire second scan. Both scans were performed under the same confining pressure of 0.6 MPa and with identical scan settings.