For El Nido Tour A, you get to either visit the Big Lagoon or the Small Lagoon but not both in one day, due to government regulations. Both are equally nice and located beside each other at Miniloc Island.
The Big Lagoon has calm, pristine waters that on a clear day you can see through. Kayaks are for rent at the entrance. Depending on the tide, the boat you are riding in may be able to enter into the Big Lagoon. Otherwise, one may either swim or kayak.