Calcite dissolution is initiated by the formation of a nanoscale etch pit followed by step edge propagation and hence strongly influenced by the interactions between surface diffusing ions and step edges. However, such atomic-scale dynamics are mostly inaccessible with current imaging tools. Here, we overcome this limitation by using our recent development of high-speed frequency modulation atomic force microscopy. By visualizing atomic-scale structural changes of the etch pits at the calcite surface in water, we found the existence of mobile and less-mobile surface adsorption layers (SALs) in the etch pits. We also found that some etch pits maintain their size for a long time without expansion, and their step edges are often associated with less-mobile SALs, suggesting their step stabilization effect.