Water has a tendency to go down.
(Everything has a tendency to go down in a gravitational field, but let's stick to water for a bit.)
Not all tendencies or biases are bad—some are useful. The water, going down from the sky, hits the ground. The water, on the ground, goes down until it finds the lowest spot it can find. Sometimes that means finding a global minimum: a wash which leads to a stream which leads to a river which leads to an ocean. Sometimes that means finding a local minimum: a puddle.
I've fixed my problems with washouts in the yard (somewhere some of my yard has found a global minimum) and now I've moved on to puddles. I don't need to eliminate them, necessarily. The part of the yard I've flattened will never be flat flat. I can get macro flatness by using a string line from the wall to the edge of the flat area. Micro flatness is beyond my ability or patience. There are slight variations on the plane—small ups, small downs.
What to do about it?
Maybe nothing. Let the cut grass take on the semblance of a flat plane.
The low spots collect water. That's OK—it's just an indication. The modified yard will shift ever so much over time as its underground tendencies assert themselves. Not all parts of the yard are compacted evenly, or made out of the same ratio of yard-local clay and imported topsoil. The yard has a fourth dimension which can only be truly known by observing it.
The low spots collect water. If they collect too much water, that's a problem because I don't want standing water, and I'll fix that local minimum with a shovelful of dirt, a boot tamp, and some grass seed. Following the water's tendencies to a problem leads to its own solution.
The water in the yard has a tendency to find a minimum. I have a tendency in the yard to create that minimum. The water is just an indication.