The Crystal River is the southernmost of the readily navigable "Big Bend region" streams. It is a beautiful body of water with, as you will see below, at least one good marina, and a fine anchorage.
I copied the text below from the Net's "Ask Your Neighbor" page (/ask_your_neighbor/ask_your_neighbor/), which was, in turn, copied from the AGLCA mailing list.

We'd like to stop at Crystal River for a day on our way down to Sarasota from Mobile, having heard that it's fun to swim with the manatees there.  I understand from a prior thread that the Twin Rivers
Marina is very shallow at the entrance (we draw 4.5 ft.) so where is a good place to stay?  Anchoring out is fine. Has anybody done this?
Advice would be appreciated.
Doug Shuman

We anchored in the Crystal River during our first cruise – see

http://www.jonahs-whale.com/Site/Shake_Down.html

There is a Google map you can zoom into which shows exactly where we anchored. It wasn't manatee season as we were there in mid-summer, but beautiful nonetheless.
Jo Stanton
Jonah's Whale

Twin Rivers Marina is not convenient to the town of Crystal River.  Continue three miles further up Crystal River and you will find a deeper alternative to Twin Rivers Marina, viz., Pete's Pier Marina or Kings Bay  anchorage.   We were there this time last year and arranged for  the dive shop to give us a pontoon tour round Kings Bay to see the  manatee.   Golden Lilly Tug docked at Pete's last month.  They  have a 4' 7" draft and said at low tide the boat was still rocking!
Alan  Lloyd
Great Loop Navigation Notes
_www.NavigationNotes.com_ (http://www.navigationnotes.com/)

There was enough water at Pete's Pier and in Crystal River for our 4.7 draft, however, you need to plan your entrance and departure to be around midtide for Shell Island which is near the mouth of the river. When we came in from the Gulf, [Tow]Boat/US heard us and the 2 other boats we were traveling with on our radios, and told us to wait an hour before navigating into the river at Shell Island. When we left Pete's Pier, we also had to gauge our departure so that we had enough water at Shell Island. [Tow]Boat/US was very helpful for local knowledge.
Barbara Benjamin
Golden Lily – Nordic Tug 42