The bay water in front of the Mayan properties are very pebbled and swim shoes make it easier to get in and out of the bay. There is just one breaker to play in and if your not carefull the wave will plow you into the pebbles. When climbing out of the bay the wave can suck you down or pull your clothing off. Sometime the wave is big and sometimes its small. Either way the pebbles are there. Also, because the marina is so close to the Mayan properties there is the strong posibilitiy that sewage and other nasty waste could infect a cut caused by the pebbles when swiming in the bay. I wear sandals and tighten my drawstring on my swim suite to be safe. I have lost and found my shorts in the wave and my wife and her friends have been topped pull down.
I'll briefly summarized what I've posted before. As background, I spent about ten years my life doing sanitary reviews of water bodies for the California public health.
I personally would not do any water contact activities in almost any beach area around the Bay of Banderas, with the possible exception of a few of the isolated beaches on the south shore. I especially would not venture into the water anywhere south of the mouth of Rio Ameca, which is the river that enters Bahia de Banderas just north of the airport (and immediately south of the Mayan Palace Nuevo Vallarta).
As a general rule, people who have been swimming and recreating in even the cleanest natural waters will show elevated levels of infections after the activity - this includes eye, ear, nose, throat, and gastrointestinal illnesses. As the water quality is compromised, these conditions get even worse.
That does not mean that I don't swim at beaches. You make tradeoffs, balancing risks and pleasure. I love to snorkel in Hawai'i, for example.
But it does mean that I grow increasingly wary as I observe and am aware of greater compromises in water quality. And there are sufficient marginal conditions throughout the Bahia de Banderas area to cause me to say the risks aren't worth it for me.