The marine area around the Cinque Terre has been a national park since 1997. We can find interesting rock formations, flora and fauna under the water as well. As I don't dive, I don't have any personal experience but I do recommend the diving center of Riomaggiore. Their shop can be found in the tunnel leading to the little fishing harbour of Riomaggiore. There are also a couple of diving centers in Levanto. They can be found on the beach, at the right end if you are facing the sea. For divers, I highly recommend a visit to San Fruttuoso and the Christ of the Abyss. Underwater life in the entire Portofino area is amazing. You can find several diving centers in Santa Margherita Ligure.
If you don't dive, you should at least try snorkeling. Make sure you have your snorkeling equipment or at least swim goggles with you. If you don't have any of these, you can rent them in the diving centers. I've seen plenty of fish off the beach of Riomaggiore and in the bay of Manarola, but my top snorkeling experience was in Paraggi.
If you prefer to be above water, why not try sailing, a boat tour from Manarola, a kayak tour along the coastline, fishing from Monterosso or fishing from Vernazza? I can also help you to rent boats or canoes, just send me an e-mail.
On windy days, Levanto is a very popular surf beach. You can find a surf school here and you can rent surf boards as well.