I have a similar situation with a small creek, rocks, sand, and culverts. You are overthinking it. Just dig a channel and lay those pipes into it at the depth you want the little pond. Put them at least a foot or two apart. Slope them a bit down - a quarter inch drop for each horizontal foot is the standard.
Then backfill with whatever dirt/sand/and rocks that you have. Use what you dug out. Yes, the material is porous, but that doesn't matter because if it is wide enough to drive across there is more than enough resistance to flow for your purpose.
This is technically called a "low water crossing" but it makes a nice little creek pond. Creek ponds are different from dug ponds. In making a creek pond you are looking to slow the flow of water which you do by increasing the resistance to flow. This is not a dug pond where you want to prevent flow with clay and concrete.
Since the cross section of the pipe is less than the cross section of the creek - and if you don't slope them too much - then a shallow pond will form naturally. You want a creek pond to "leak". It's healthier that way.
You can change the depth of the pond a foot or more by either restricting the flow into the pipes or by adding another pipe. For restricting the flow, just placing one big rock in front of each pipe will make a difference. Again, you are just increasing the flow resistance. Not flow prevention.
Do it with what you have and you'll be done in a weekend. Mine isn't much larger than a game room and you would be amazed at the wildlife and plants it supports.
Good luck,
rScotty