I've never used Polywater, but I have used duct seal before (trade name "monkey shit") to seal conduits that have water leaking through them. Check out panduit or pug duct seal. I'm not sure if its UL listed, but its been used by electricians for decades.
As far as what Grover mentioned, it sounds like an existing installation that could be getting water from about anywhere, and its probably not within the scope of the job to go and find the leak, and depending on system size that could be a big job. However, if you do know where the water is coming from, I'm with Grover, I'd fix the source instead of sealing them at the pumphouse.