It's better to buy a dedicated waterproof USB connector. They are available as a set. Some of these types of USB connectors support data transfer.
The female USB port is usually mounted on a panel and the inside portion accepts a male USB cable. This portion will need to be sealed, one could use hot glue, silicone etc.
When the USB cable needs to be used, one would unscrew the cap off the female USB socket, insert the male USB plug and then screw the waterproof housing on the male USB cable to the female connector.
The male USB are mostly available with mirco USB on the end that plugs into a device. There are also Type C cables available.