Reasonable pet deposits and fees for renters?

I'm new to the state and found an apartment that I'm all set to sign a lease on, but I want to make sure I'm not being taken advantage of. For one thing they charged me $120 between the application and admin fee (50 and 70 respectively, both non-refundable), and quoted me a $250 refundable security deposit, plus $150 non-refundable pet fee and $10 monthly pet rent. I also pay my water with my rent, but it's an additional amount based on usage. Then when they found out I'm on section 8, they said my deposit would be $500 instead of $250, with everything else remaining the same. Now that the unit has passed inspection and it's time to sign the lease, they backed down the deposit to $350, but that's still 100 more than it would be were I not receiving assistance.

Based on my initial research, they aren't allowed to ask for a higher deposit due to being a section 8 recipient, so I'm wondering if I should hold them to the law or not. I assume that if I do, they could easily just decide not to rent to me at all. Is that correct, or am I protected by law in that regard? Also, a non-refundable pet fee in addition to monthly pet rent seems like a bit much. Shouldn't it be one or the other, or at least a refundable pet deposit plus pet rent instead of a non-refundable fee plus pet rent? Finally, how do I ensure I'm not being ripped off on the water bill, since it's being metered by the complex instead of a utility company?

Any help or advice is much appreciated.