Depending on your filtration set up, I would highly recommend tossing any/all filter media that may have been sitting without water flow. Carbon, filter floss, resins and the rest. They will be completely contaminated with decaying matter. Some may be able to be rinsed well and re-used but be very careful.
This is especially important to those that use canister filters. After a few hours of being shut off, they should be discinnected from the system and thoroughly cleaned.
I would do a good size water change and possibley add a bit of ammonia binder to the water. Once the tank is back up to normal water flow, it should come into line quite quickly. Keep close tabs on things though.
Best of luck!