Not in the harbor itself, but there is a public beach at the mouth of Sister Creek that is popular, and what we in the Harbor refer to as Gilligan's Island, which is also located near the mouth of Sister Creek.
The harbor's waters are relatively clean and swimming would not be a problem if it were not for the occasional bull shark that tends to lurk among the boats on mooring balls. A couple guys dive in the harbor and clean boat bottoms, and it's rare for them to see a shark.
One of the great things about Marathon is this particular key is not one that the spring breakers head to - it's nothing like Key West and has lots of activities for folks that fit into the retirement category. Just off the beach at Sombrero Light there are mooring balls for snorkeling and the underwater visibility averages about 30 to 40 feet.
On days when the weather cooperates, I day sail on the gulf side of the key and enjoy the pristine waters.
Many good to excellent restaurants in town, plays nearly every night, lots of nite-life locations, and something going on nearly every night at the Marathon City Marina's Tiki Hut, including Saturday night jam sessions of which I'm a part of from January through mid March this year, and November through March this coming winter if I can manage to keep healthy enough for the trip down.
Get the Hell out of the snow belt, C'mon down to Paradise - Boot Key Harbor is a nice place to spend the winters.
All the best,