I've done this mission a few times and here's what really works - start by playing as naoe and make sure you've got the shallow water breathing skill unlocked in your shinobi tree, it's pretty much essential. When you get to the water areas, the basic idea is to stay low and use those reeds scattered around to hide and breathe. Something interesting about the breathing reed, you can actually use it to completely vanish from guards' sight if you time it right.

The main thing to remember is staying in prone position while swimming, and whenever you spot patrols, use observe to track their movements before making any moves. You'll find plenty of underwater caves and rock formations that make perfect hiding spots, especially near places like nishinomiya shrine's lake or the swamps around mangetsuji temple. Speaking of which, if you're going after someone like the godai of water, those swampy areas are perfect for sneaking up from behind.

A really helpful tip - when you're spotted, don't panic and swim straight away, instead dive deeper and look for those underwater caves to break their line of sight. Once you've done whatever you needed to do whether that's grabbing something or taking someone out make your escape through hidden tunnels or surface near reed beds. You might want to upgrade your oxygen-extending skills too, they make everything much easier especially during longer underwater sections.