When you’ve got a flat roof and have found a pool of water up there you should be concerned because flat roofs are made to slope to the drains to keep the roof free from puddles.
You’ve got a low spot for a reason. The sagging could be happening on account of the joists being too far apart or improperly sized or worse yet, there could be a leak causing decay of the wooden joists.
For do it your self types, you need to pry up the plywood and look underneath it, check out the joists and find out if they are too far apart or if they’re decaying. Once you have sorted out the joist trouble, nail down new plywood and re-roof the area.
We know those who would do this on their own by adding material to raise the low spot, but the extra weight could result in more problems instead of fixing your original problem. If you wish to choose that route hire a structural engineer to make sure you have a green light for the added weight on that area of your roof.
The best thing to do obviously is hire someone familiar with this, like a roofing company. Most roofers offer a good work warranty and referrals you can check out.