I add about 3/4 cups of Blue Diamond almond milk (unsweetened) every morning to a single serving of Cheerios. The milk contains filtered water, and I read that drinking water with food at the same time makes it harder for the small intestine to absorb the nutrients from the food. Has this been verified?
Overall, no it doesn't. Cereal is made in a way that it's expected consumers will consume it with milk. Here's a list of some important fortifications added to cereal and milk effects on absorption.
Riboflavin: No. Affected most strongly by light.
Iron: Yes. Calcium can affect absorption. Milk causing a deficiency is rare unless it is being used as a breast milk substitute in babies.
Thiamin: No. Unless you are drinking alcohol with your cereal.
Folic acid: Milk is a source of this!