The 3k3 with 1µF is a 48 Hz filter. When that is a electrolytic capacitor, it might leak.
Are the pump 12V and used in parallel at 9V ? That is okay.
Is it possible that the (ground) current of the pumps might influence the sensor ?
I would remove the RC filter and try an other filter in software. But every filter will make it slower.
When that does not help, perhaps a damper chamber might help.