Step 1: Go to Appearance > Customize > Layout > Header Layout.
Step 2: Use the Header Mode radio buttons to choose Transparent.
This will make your header fully transparent. If you want only some transparency, you can obtain this effect by adjusting the navigation color:
Step 1: Go to Appearance > Customize > Colors > Header > Navigation Color.
Step 2: Click on the Select Color button and use the right most vertical slide bar to drag to a transparency percentage. You can also use the field to type a value for the color. For example, rgba(255,255,255,0.5) will give you a white navigation with a 50% transparency.