Southwest of the town of Crystal River, the snorkeling in the Crystal River estuary is known for the encounters with West Indian Manatees. The area just west of Crystal river is known as Kings Bay and is protected as the Crystal River National Wildlife Refuge. While Kings Bay snorkeling is good year-round, there are more manatees in the Winter months (January and February), but the summer months are less crowded with snorkelers. During most weekends, the Crystal River is absolutely crazy with boaters, so if you are planning a manatee snorkeling experience you will want to come early on a weekday (the 7am trips are usually the best).
Kings Bay has a fully developed coastline with a shockingly high number of boat docks lining the shore. While the bay is spring fed, it is more like a shallow lake with significant algae and plant growth. The water clarity in the Crystal River will definitely impact your experience. Contrary to the name of the river, the Crystal River isn't always crystal clear. The best visibility is usually found in the winter months, especially if there hasn't been rain for several days. By late March and April, the warming water and afternoon rains significantly reduce visibility. It is not unusual for the visibility to be well under five feet, especially within 24 hours after rain. There will be occasions when the visibilty is so poor, you will not be able to see anything more than a foot in front of you.
In order to snorkel with the manatees, you will most likely need a boat. While you could rent a kayak and try to snorkel off the kayak, the best experience will be to use one of the numerous charter dive boat operators. For most of these guided tours, it is highly recommended to make a reservation far in advance and try for the first trip of the day on a weekday. Make sure to reconfirm your reservation the afternoon prior to the trip since the boat tours usually require a minumum number of passengers to go out. Ask how many reservations they have and what the minimum number is required. They are known to cancel without notice.
When snorkeling with manatees, it is recommended to wait for them to initiate contact; only touch them if you are touched first to avoid scaring them off. Also, unlike many of the videos you may see about snorkeling with manatees, the manatees are usually only stationary in the early mornings in the winter months. Otherwise, they are on the move, especially during the Spring mating season. This results in a lot of swimming for the snorkelers to keep the manatees in sight, so you'll want to be a good swimmer and in good shape to keep up.
TIP: the water temperture is usually in the low-70's, so a wet suit is recommended.
Overall, Crystal River is the 6th most popular snorkel dive spot of all 18 snorkeling dives in Florida Gulf Coast.