I've been wracking my brains on this, going so far as to dig out books from a box of previously read books in my basement. Not the most sure way for me to find the book, since I give many away after I'm done with them. But there are still some left in that basement box.
Two I found there, I cannot remember the plot line. "Deep Fathom" by James Rollins and "Deep Storm" by Clive Cussler. So I looked those up on Wikipedia. This sounds somewhat familiar, regarding "Deep Fathom":
Quote:
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...Undeterred by earthquakes, they escape from patrols and get to the boat which Karen had hired to take them to the twin dragons, submerged pyramids which had come above the sea level along with a whole city. When they get there they go to a large pyramid to explore but are interrupted with three men come from nowhere and ask them to leave. The women refuse and after being chased deep into the pyramid, they find a star-shaped crystal. Using the crystal, the women escape and return to Okinawa...
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This seems to match my "partially submerged stone structure" recollection. And then I found some references to Clive Cussler novels, the "Oregon Files" series specifically, protagonist Juan Cabrillo, who (possibly?) preferred a 5.7 handgun. I remember reading one book from the Oregon Files series (I think), but I can't remember which one. So maybe I am indeed confusing two separate books into one in my mind.