Thanks for taking the time to reply jml755. I apologize if this comes across as rude and I do not mean to be rude, but your response seems as if all you did was look at the pictures of my post. I'm well aware of the source of the problem; I even clearly stated that in my previous post, and I'm looking for solutions to do the job properly. I'll explain a little further what my experience has been when the cages are just removed while the creek bed is loaded with silt and debris. Simply removing the cages allows all of the debris to flow freely into the pipes. The pictures may not show clearly the extent of debris that have gathered at the entrance of the pipes, but I will explain. Large limbs and sticks are among the debris and they get hung inside the pipes. After these debris get caught they add to the problem by catching leaf litter and more silt. I do not wish to go through this experience again using just my hands and hand tools.
I do not want to discourage anyone from posting helpful details, but I know from experience that simply taking the cages off will not solve the entire problem. That is likely the first step, but before I do so I will need a plan to work the debris through.