Most papers, documents and books can be cleaned and air-dried using the following steps:
If the damage is from dirty flood water, gently rinse the papers in a bucket or sink of clear, cold water. If they are especially fragile, trying laying the papers on a flat surface and rinsing with a gentle spray of water.
Lay the papers individually on a flat surface, out of direct sunlight. If the papers are soggy, lay them in piles to dry out a bit before attempting to separate them. If space is a problem, try stringing fishing line across the room and use it like a clothesline.
Use an oscillating fan in the room where your papers are drying to increase air circulation and speed drying. (Aim the fan at the floor. The idea is just to stir the air slightly.)
For water-logged books, the best option is to place absorbent paper between the wet pages - "inter-leaving" - and lay the books flat to dry. You don't have to place blotter paper between every page, just every 20-50 pages or so. Change the blotting paper every few hours.
If you have wet papers or books that you just can't deal with right away, then seal them in Ziploc-type bags and stick them in the freezer. This stops the deterioration of the paper.
Remember, books and papers don't have to be directly in the water to suffer damage. The extra humidity from all of the water in the vicinity is enough to trigger the growth of mold. It is important to remove your books and papers from the wet location as soon as possible.
After your papers and books are completely dry, they may still suffer from a residual musty smell. To combat this, place the papers in a cool, dry place for a couple of days. If the musty smell still lingers, put the books or papers in an open box and put that inside a larger, closed container with an open box of baking soda to absorb odors. Be careful not to let the baking soda touch the books, and check the box daily for mold.
If you have important papers or photos that develop mold, have them copied or digitally scanned before discarding them.