What brand/ model are the boots? Were they sold as waterproof?
A lot of trail shoes and boots are designed to drain well, so as to keep feet ventilated in dry conditions, or to drain excess water in deluge conditions, they are deliberately not waterproof.
In very wet conditions, even wearing gaiters may not keep you 100% dry in waterproof boots. If I'm doing something very long in wet conditions, I'll often go with non-waterproof footwear as waterproof boots will lose all breathability as the exterior becomes waterlogged, and between the sweat build-up and water coming in over the tops, you're better off with damp, rather than waterlogged feet. Staves off trenchfoot for longer. Merino socks help too, as does covering feet with sudocrem.