The process of electrical discharge micro-drilling (micro-EDD) of micro holes is used in the aviation, automotive and biomedical industries. In this process, an important issue affecting the stability and efficiency of the process is the flow of the working fluid through the tool electrode channel and the front and side gap areas. Because tool electrodes have diameters below 1 mm. Many factors present in the EDM-drillig process occurring on a micro scale mean that a full explanation of the phenomena affecting the process is limited. The solution is to analyze the phenomena in the process based on the results of numerical simulations, which are based on real measurements. The aim of this work is to analyze the flow of de-ionized water through a brass single-channel electrode with a channel diameter of 0.11 mm and a front and side gap. The liquid flow was analyzed for various variants (with and without cavitation, with added rotation of the tool electrode, with and without surface roughnes with material particles). In simulation, it is important to gradually increase the complexity of the model, starting with the simplest model and gradually adding further phenomena. Analysis of the simulation results showed a significant impact on the liquid flow of cavitation, as well as the presence of vortex gaps in some areas, which have a significant impact on the process of drilling micro holes.