UNESCO World Heritage Sites = AMAZING! Though you could easily spend weeks in the Shark Bay Heritage Site, on your first trip, be sure to at least spend 3 days. It's a good hour plus from the main road, be sure to get fuel before heading in.
First Stop: Stromatolites. These incredible organisms are how life began here on earth. They are, in my most humble opinion, simply too cool for words. A must see and worthy of an hour or so of time.
Next up: Shell Beach. One of the only beaches in the world with no sand, only hundreds of millions of tiny white shells. Consistently rated one of the best beaches in all of Australia. If nothing else, worth a dip in the water and reading up on how this phenomena also helped create many of the buildings in the closest town, Denham.
You could easily drive right by the Ocean Park Aquarium, but I recommend stopping in. Not only are the critters engaging, and the Shark feeding pretty darn exciting; the best deck in the area juts out over the Indian Ocean, providing stunning views, especially at sunset.
Denham may be where your accommodation ends up for the evening, with a plethora of options in this tiny town of about 600 residents. While here, be sure to visit Debbie at the Shark Bay Discovery Center. You can easily spend a few hours roaming the many exhibits and chatting with staff.
Though you have most likely already paid for your Western Australia Parks Pass, be prepared when you arrive into Monkey Mia, to pay an additional conservation fee. Don't fret, it is well worth it. With a fabulous restaurant and housing options, emu and storks wandering the grassy park areas, and dozens of dolphins who come in to interact daily along the shore, you can't go wrong in this bucolic seaside conservation area.
If you are feeling adventurous and are already driving a high clearance 4-WD, taking a full day and heading into Francois Peron National Park, is a stunning way to end your stay in this World Heritage area. Should you not feel confident in your driving ability or lack of aptness to reduce and again inflate your tires, there are a number of local naturalists who can take you into the park and really give some fabulous insight on the many bays, look-outs, flora and critters, you can encounter while here. Additionally, at the homestead just at the beginning of the park, there is a lovely 24 hour access natural hot springs, for you to relax your weary body.
You are about a 6 hour drive to Coral Bay and the Ningaloo Reef World Heritage Site, bear this in mind when deciding to leave the Shark Bay area. It is not recommended to drive from sunset through dark. This is when kangaroos, cattle, camels, emu and large lizards tend to take up road space, which can be quite dangerous whilst driving in the outback.