I am certainly no expert on the permit process but I have tried it twice and thought I'd share my experiences. I currently have a pond under construction (see "my first pond" on selecting a site). With that one I started by talking to the local conservation office and they said since I was not in a protected area and was basically excavating out an area to catch rainwater (there is only water flowing in the area after the snow melts or heavy rain periods)I did not need any permits. They did tell me to talk to the Dept of Transportation because it would be close to the highway so I did that and they said no problem because I was not building a dam and there was already a culvert under the road designed for the area. So as far as I know this pond is legal and I did not need any permits. Technically I guess I could have done this pond without even checking with anyone but I didn't know that at the time.
On the second project I have a creek that runs through my land, the creek flows all year and varies from 12-24 inches deep and 4-6 feet wide. My plan is to excavate a pond along the creek and then cut into the creek and divert some of the water into the pond and then at the other end of the pond have the water flow back into the creek. I again started at the conservation office and they said on this one I would need to check with the Iowa Dept of Natural Resources because I may be in a protected wetlands area. I called the number they gave may and the gentleman I spoke to said that I was not in a protected area so I could dig there. He also said that I would need to talk to the "water rights" part of the DNR and gave me the number. I again explained to project to tha guy and he said that as long as I was not stopping the flow of the creek I was ok but that I would need to have a "water storage permit" He sent me the paperwork, which was a single page with just some generic questions and a description of the project. That gentleman was the first person that said anything to me about the Corp of Engineers. He said that his understanding was that the Corp would not have a permit that I would need for a project like this but he recommended calling just to be sure. I called the number that he gave me and once again explained the project. The gentleman at the Corp of Engineer explained that essentially the corp regulates the placement of soil into waterways (building dams on creeks, filling in wetlands,...). He explained that since I am not putting soil into the waterway I did not need a permit from the Corp of Engineers. So again as far as I know this pond will be legal and the only permit that I will need is the water storage permit because I will be confining some water.
I don't know if this will help anyone but just thought I'd share the information.