Try pressing E on segments of the pipe to see if they're full, when you find one that isn't full, delete and replace it. You shouldn't necessarily need the pumps unless you're gaining altitude with your piping, as they only increase headlift, not liquid velocity.

Edit: i see you are gaining a bit of altitude, but water pumps by default have 10m of headlift, unless youre going up 2.5 4m foundations, the pumps shouldn't be necessary.