The town’s small but excellent Museo de la Isla de Cozumel (Av. Rafael Melgar at Calle 6, tel. 987/872-1434, 9 a.m.–5 p.m. Mon.–Sat., 9 a.m.–4 p.m. Sun., US$3) is on the waterfront in what was once a turn-of-the-20th-century hotel.
Well-composed exhibits in English and Spanish describe Isla Cozumel [1]'s wildlife, coral reefs [2], and the fascinating, sometimes tortured, history of human presence here, from the Maya pilgrims who came to worship the fertility goddess to present-day survivors of devastating hurricanes.
Be sure to visit in the morning if you want to avoid the cruise ship crowds. The museum also has a small bookstore, a library, and a pleasant outdoor café overlooking the sea.
Links:
[1] http://www.moon.com/destinations/cancun-the-yucatan/cancun-cozumel-and-the-riviera-maya/isla-cozumel
[2] http://www.moon.com/destinations/cancun-the-yucatan/cancun-cozumel-and-the-riviera-maya/isla-cozumel/sights/coral-reefs