How fast is the water flowing? Is there a time when it's not flowing?
Does the creek have a name? Here in Texas, you can dam up a creek if it's not named, but if it's named, you have to get permission from the Dam Authority for that area. Seems like every Dam has a claim to every named creek.
As mentioned already, rocks are very bad in a dam. They allow water to flow around them. It's the same thing that happens to roots from a tree.
If you want to do this, you need to remove all the rocks, then dig down below the bottom of the creek, and into the shoreline of both sides. How much you have to remove depends on how big the dam will be. I forget the rule of thumb, but the idea is the weight of the water should push down on the dam more then it pushes against the dam. Then you want to build the dam of compactible clay. Here in Texas, red clay is the best for this. Compacting the clay is critical because it needs to be solid enough to keep water from penetrating it. To do this, you add the clay in lifts, then spread it and compact it. The best tool for compacting is a vibratory sheepsfoot roller. You want as much weight as possible, but you also want to mix it a little as you compact it. I personally use the front tires of my backhoe, with a yard of dirt in the bucket to compact my red clay. I can see the tires sink into the clay when I start, but it quickly becomes solid as I go over it. Then I dump the bucket, spread it, get another load of dirt, and drive over the clay all over again.
Once the dam is where you want it, then you need to dig out the dam to install the pipe. It will be very hard to compact the soil around the pipe, so try to remove as little soil as possible. Water will want to run along the sides of the pipe, so the better your compaction, the less likely it will leak under the culvert. I like to put concrete around both ends of my culverts.
The biggest issue will be where the water exits the culvert. The water come out of it will erode below, and then under the pipe. This is where you want to put all your rock. The more the better!!!!
Since you can never predict how much water you will get during an extreme storm, you need to have an emergency way to deal with more water then the culvert can handle. You can either dig a wide shallow trench off to the side of the pond to direct the water around the dam, which would be the best way to do this, or you will have to have a hard surface of some kind to allow the water to flow over the dam, which will be the expensive way to go, and what will probably eventually lead to the failure of the dam.
Most creek dams eventually fail. I wouldn't dam up a creek, it's very involved, very expensive, and rarely works out. Both of my ponds are far enough away from creeks to avoid flooding. I've put in roads with ditches on my land to carry water to my ponds. If you really want a pond, walk around during a heavy rain and watch what the water is doing. This will give you an idea of where to dig, and how big you can make the pond.
