Must stems be submerged?

I have a hardy water lily in a 1-gallon container, which is in a pond. The pond reaches the top of the container (barely) and the leaves reach the water, but the stems are not fully submerged. Will the water lily survive and be happy? And bloom? I'm in zone 9. Thanks. P.S. Should I transplant the water lily to a more shallow container, so the stems will be fully submerged?

Doug says that he hopes you have a tropical waterlily rather than a hardy one because the hardy plant is going to require a dormancy to get it to rebloom. It will slowly fade away with a cold dormancy.

And yes, you need to plant either of these plants more deeply to the requirements as listed on the page. They really want to be down a minimum of 12 inches to 18 inches in ideal conditions.

To make your life even more difficult, a one-gallon container is far too small for a waterlily. It will (and should) outgrow that container in a month or two after you put it in the pond.