You just have to be careful of the rocks you choose/find. Assuming you are not talking about gravel substrate:
For example, limestone will raise your ph, and there are other rocks which will put minerals in the water such as iron. There's sandstone but it often becomes flakey and will make your water dis colored over time. Slate is the best. The cheapest way to go (other than slate) is the pond pebbles at Home Depot (I think the brand name is Vigaro). With any stones or rocks be aware of sharp or jagged edges as you don't want a fish being chased to injure itself in an accidental collision.