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