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

If you don't already know it, let me be the first to tell you, the Big Bend region of the Western Florida coastline (north of Anclote Key to Carrabelle and Dog Island) is not served by any sort of intracoastal waterway. So, you must choose to either cut the corner, or, staying WELL offshore, follow the Big Bend coastline around. If you choose this latter course of action, Capatin Doug's plan below has REAL merit!

Steinhatchee isn't much, but it's a good place to go to get across the gulf 70NM or so.  Then a nice cruise day is to go from Steinhatchee to Yankeetown.  Yankeetown is a teeny sleepy town, very non-touristy and not much to see, but the 10 mile trip up the river to Yankeetown is really very interesting.  The river is 10 to 20 ft deep all the way, with interesting narrow bends and changes in scenery from salt marshes and palm trees at the gulf followed by hardwood forests overhanging the river at every turn.  Then you go to Crystal River the next day. It's only 10 NM or so and you get there for lunch, swim and watch manatees that afternoon and you're ready to go to Tarpon Springs the next morning.
Doug

I copied the very useful discussion below from the AGLCA list. Crystal River is one of the southermost of the Big Bend River, found north of Homosassa River. Note the data about shallow water at Twin River Marina. I join with Captain Alan below in recommeding that cruisers continue upstream to Pete’s Pier Marina, or try anchoring in Kings Bay.

We were told there was enough water to come into Twin River Marina, however, boats sit on the bottom at low tide. Any boats with a draft over 3.0. will have a problem. I always ask about draft and channel clearance, and was told no problem. That has not been the case.

We draw just 2’10” maybe 3′ when fully loaded and would concur that spots can be a bit shallow. We commented a number of times going in, that big boats would have a hard time getting into Twin Rivers Marina. Even at our depth we stirred up some mud. Take care as it sure is worth the effort to be able to swim with those Manatees. For me one of the high lites of our whole trip.
Clare

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 a pontoon tour round Kings Bay to see the manatee.
Alan Lloyd
Great Loop Navigation Notes

We’re docked at Pete’s Pier Marina. Good to be off the Gulf while the next system moves through. We planned on staying just one night, heading to Clearwater this morning, but the system is moving through faster than the forecast indicated last night. The staff here are great. This marina is in walking distance to town, had a wonderful meal last night at Cody’s. Enterprise is right around the corner too.
Denny and Karen
Another Option

Click Here To View the Western Florida Cruisers’ Net Marina Directory Listing For Twin Rivers Marina

Click Here To View the Western Florida Cruisers’ Net Marina Directory Listing For Petes Pier – Kings Bay Marine

I’ve said it before, but it’s worth repeating. Get any four cruisers together, and you’ll get six opinions about how best to cross the Big Bend region of Florida, between Apalachicola or Carrabelle, and Anclote Key (or Clearwater). For those of you not familair with these waters, there is NO protected intracoastal waterway serving this portion of the Florida coastline. So, the decision is whether to cut the corner and head straight for Anclote or Clearwater, or follow the Big Bend coastline around, staying SEVERAL miles offshore to avoid the long shelf of shallows that run out from this part of the Florida coastline. There are those who believe passionately in one or another of these plans.
I have copied the discussion below from the AGLCA list in hopes that others thoughts may aid you in your own decision!

You are correct that many cruisers leap across the arm pit in a single bound. From Carrabelle to Tarpon Springs is 170 statute miles. For most this translates to an overnight trip. If you do not wish to go overnight, or like me, do not have the range, it is better to do shorter runs with more stops.
The first leg is from Carrabelle to Steinhatchee, 85 miles. From there it is 120 miles to Tarpon Springs.
I recommend an intermediate stop at Crystal River. The entrance to Crystal River can be shallow but if you draw less than 4.5 feet it is doable.
Best to avoid Homosassa River and Suwannee River unless the latter is dredged before the date of your trip.
These are the routes are described in my book .
Alan Lloyd

The “Big Bend” is a very nice part of the trip and missed by too many loopers rushing for unknown reasons. It’s an “old Florida” pace and style. Wait for good weather to go from Carrabelle to Steinhatchee, next day go the sort trip from Steinhatchee to Yankeetown, because the deep narrow river trip up to Yankeetown is really cool. Then go 20 miles to Crystal River to see the manatees, and finally go 55 NM to Tarpon Springs.
Doug Shuman