In a large bowl, using an electric mixer, beat together butter, peanut butter, brown sugar, and vanilla until creamy. Beat in eggs and water.
Mix together flours, oats, wheat germ, salt, cinnamon, and baking soda.
Mix into peanut butter mixture. Stir in raisins. Drop by ice cream scoopfuls 2 1/2 inches apart on greased cookie sheets. Flatten slightly.
Bake at 350 degrees F (175 degrees C) for 18 - 20 minutes. Cool on cookie sheet for 2 minutes, then transfer to cooling racks. Store in an airtight container.