but the lilies are protecting my water levels
I feel that the lilies really may be making the difference.
I would like to eradicate the hydrilla but keep the lilies.
How are the lilies (undoubtedly American lotus) protecting the pond's water level?
As for mechanically "controlling" hydrilla, understand that hydrilla is one of the few invasive species that just might be capable of creating a 110% infestation (or so it would seem). Keep in mind the source of Hydrilla's name: The Hydra, in Greek mythology, was a monster with nine heads, each of which, when struck off, was replaced by two new ones.
I'm certainly not against American lotus, providing it doesn't get out of hand. In fact, lotus makes excellent cover - especially its shade.
I'd suggest a low-dose (10-15 ppb) fluridone treatment next spring (Mar/Apr), which should control the hydrilla - and possibly thin the early-season lotus crop (from seed germination). Then, if needed or desired later in the season, use a targeted/topical application of glyphosate, imazapyr or 2,4-D to treat corridors through the lotus - to produce great "weed edge" fishing.