We use electrochemical scanning tunneling microscopy (EC-STM) to image single-crystal surfaces of the layered bismuth chalcogenide Sn0.01Bi1.99Te2Se in situ under electrochemical control for the first time. The Bi chalcogenides are of interest for their thermoelectric properties and as model topological insulators (TIs). We show that oxidative dissolution takes place via the progressive nucleation of pits in the initially smooth surface terraces rather than at their edges. Nanometer-resolution EC-STM images show that the pit depth is generally equal to the thickness of a complete chalcogenide quintuple layer. The preferential redeposition of dissolved components at step and defect edges on application of a more negative potential after oxidation is observed. Our work demonstrates the ability to control and characterize the surface morphology of single-crystal TIs in an electrochemical environment.