Should I dig in the muddy soil?

I built a little trench in my backyard for water drainage. I used my level to make sure the perforated pipe was angled downward. I placed dirt and sod over it and during a rainstorm the trench does a good job for the most part but near the end the water pools up so I think I need to make the angle a little deeper near the end of the pipe. The problem is that it has been raining nearly everyday so there is no time for the soil to get dry enough for me to dig. I want to try and get it done to prevent the stale water from attracting mosquitoes and before the sod grows into the lawn. So I guess it is ok to dig into the mud, the only negative it being really messy?