Super Resolution (SR) imaging has the potential of visualizing the micro-vasculature down to the 10 μm level, but motion induced by breathing, heartbeats, and muscle contractions are often significantly above this level. The paper therefore introduces a method for estimating tissue motion and compensating for this. The processing pipeline is described and validated using Field II simulations of an artificial kidney. In vivo measurements were conducted using a modified bk5000 research scanner (BK Medical, Herlev, Denmark) with a BK 9009 linear array probe employing a pulse amplitude modulation scheme. The left kidney of ten Sprague-Dawley rats were scanned during open laparotomy. A 1:10 diluted SonoVue contrast agent (Bracco, Milan, Italy) was injected through a jugular vein catheter at 100 μl/min. Motion was estimated using speckle tracking and decomposed into contributions from the heartbeats, breathing and residual motion. The estimated peak motions and their precisions were: Heart: Axial: 7.0 ± 0.55 μm, Lateral: 38 ± 2.5 μm, Breathing Axial: 5 ± 0.29 μm, Lateral: 26 ± 1.3 μm, and Residual: Axial: 30 μm, Lateral: 90 μm. The motion corrected micro-bubble tracks yielded SR images of both bubble density and blood vector velocity. The estimation was, thus, sufficiently precise to correct shifts down to the 10 μm capillary level. Similar results were found in the other kidney measurements with a restoration of resolution for the small vessels demonstrating that motion correction in 2-D can enhance SR imaging quality.