Pandoc, the GNU make and sed commands, sprinkled with some CSS are all you need to fully automate the creation of a static website starting from Markdown.
Pandoc offers three command line options which can provide navigation between pages as well as the creation of a table of contents (TOC) based on the headings inside the page. With CSS you can make the navigation and TOC look and behave the way you want.
-B FILE, --include-before-body=FILE
Include contents of FILE, verbatim, at the beginning of the document body (e.g. after the tag in HTML, or the \begin{document} command in LaTeX). This can be used to include navigation bars or banners in HTML documents. This option can be used repeatedly to include multiple files. They will be included in the order specified. Implies --standalone.
--toc, --table-of-contents
Include an automatically generated table of contents.
--toc-depth=NUMBER
Specify the number of section levels to include in the table of contents.
The default is 3 (which means that level 1, 2, and 3 headers will be listed in the contents).
As a matter of fact, my personal website is built this way. Check out its makefile for more details. It is all free-libre open-source licensed under the GNU GPL version 3.