While all the incidents I've observed appear coincidental, I'm not keeping any "BIG" snakes, & the more I thought about it, I think it's entirely possible that some species that evolved near water may intentionally use this method to help subdue their prey. As I recall, crocodiles are known for pulling prey underwater, & that gives them an advantage, so I don't doubt your observation. It still could just be a "one-off" though- time will tell & if you see this happen repeatedly, be sure to update us.
It very well could be instinctive, & even when snakes are fed only dead prey, they still mostly act according to instincts. (For example, rattlesnakes fed only dead prey long-term still bite their prey to envenomate it, even though it's not needed.)