Nickel-based superalloys are being increasingly applied to manufacture components in the aviation industry. The materials are classified as difficult-to-machine using conventional methods. Nowadays, manufacturing techniques are needed to drill high aspect ratio holes of above 20:1 (depth-to-diameter ratio) in these materials. One of the most effective methods of making high-aspect-ratio holes is electrical discharge drilling (EDD). While drilling high aspect ratio holes, a crucial issue is the flushing of the gap area and the evacuation of the erosion products. The use of deionized water as the dielectric fluid in the EDD offers a considerable potential. This paper includes an analysis of the influence of the machining parameters (pulse time, current amplitude and discharge voltage) on the process performance (drilling speed, linear tool wear, taper angle, hole’s aspect ratio, side gap thickness), during the EDD with the use of deionized water in the Inconel 718 alloy. The obtained through holes were subjected to the extended analysis. The impact of the initial working fluid temperature and pressure on the conditions of the flow through the electrode channel was also subjected to the analysis. The deionized water properties were changed by applying an initial temperature. Based on the results of an analysis of the previous research, the EDD of the through holes was performed for a pre-set initial temperature (~313.15 °K) and initial pressure of the working fluid (8 MPa) and selected process parameters. An analysis of the results indicates increasing of hole’s aspect ratio by about 15% (above 30), decreasing the side gap thickness by about 40% and enhanced surface integrity.