A novel method to fabricate nanoscale pits on Au(111) surfaces in contact with aqueous solution is claimed. The method uses in situ electrochemical scanning tunnelling microscopy with independent electrochemical substrate and tip potential control and very small bias voltages. This is significantly different from other documented methods, which mostly apply high and short voltage pulses.The most important advantages of the present method are that the high precision in aqueous environment so that nanoopatterns of the pits can be designed, and that the operations are simple and require no instrumental accessories. Parameters, which control the pit formation and size, have been systematically characterized and show that the primary controlling parameter is the bias voltage. A mechanism based on local surface reconstruction induced by electronic contact between tip and substrate is in keeping with the overall patters for pit formation. A range of potential applications is proposed.