I've never tried growing tomatoes myself; but I've read on the water gardening forum, that some people grow tomatoes in their pond. So my guess is that your tomato plant is doing what it really enjoys doing... getting itself a nice big drink of water.

If it was a problem for the tomato, it wouldn't be there. Kind of like air pruning...if water was harmful, the roots would just die when they hit the water. Actually, you can break off tomato suckers in summer and toss them in a bucket of water to root for planting out in the garden for a fall tomato crop.