Hurting knees is my first sign of too much of load that I am carrying. I don't have access to a pool, I'm a little envious of that, but I find just walking, and walking some more - and I love Leslie Sansone's WATP DVD's - do the trick for me. Add some Fish Oil supplements and it's amazing what difference a few days can make. I wish you well!
"My body is the temple of the Holy Spirit who is in me, whom I have from God, and I am not my own. For I have been bought at a price, therefore I will glorify God in my body and in my spirit, which are God's."
(paraphrase of I Cor. 6:19-20