While staying at the Icon Vallarta (next door to the new Hilton Hotel) guests were warned by several residents and employees not to swim in the ocean as a crocodile had been seen swimming in the waves and waddling on the beach recently.  This was in late September/early October 2012.  Although many people who live in the area will claim that these sightings are "hogwash" - there have been reports that never make to to the papers of real crocodile sightings in tourist areas.  Many crocodiles have been spotted at The Marina as this was their home before the Marina was built.  As tourism is bad enough in Mexico, the last thing they need is bad publicity regarding crocodiles swimming in the ocean.  They do end up there as the River Cuale empties right into the ocean in the center of Puerto Vallarta.  Although  no incidents occured people do swim in the ocean frequently.  However there is reason for concern in that  often there were no swimmers at a very popular tourist beach.   People don't stop going to the beach because of shark attacks (despite the horror of JAWS) and they shouldn't stop going to Mexico because of one or two lost crocs.  But, to be on the safe side - don't swim alone and please keep an eye on your pets and kids.

All the rivers empty into the ocean.

The Rio Cuale unfortunately doesn't have enough water to satify a crocodile, the Rio Ameca, on the other hand has plenty of both and it is from here, plus the University of Guadalajara's crocodile preserve north of the airport, that the occasional one will venture into the bay, looking for a new home. The American Crocodile is not as agressive as your Floridan Aligator, which has quite a reputation of eating people, doesn't seem to bother their tourist industry.

PV hasn't lost one, yet. A couple of limbs have been lost by locals not being very careful, but never in the ocean. Golfers at the Marina Course are advised to not go looking for balls hit into the water hazards. :)