According to my mental arithmetic, with the components you specify, that circuit will oscillate at upwards of 50 kHz. If you are using silicon power diodes of the 1N4004 sort, they cannot switch at (anywhere near) that speed, so they capacitively load the circuit instead of rectifying. I think you might do a lot better using 1N914/ 1N4148 diodes and 1µF capacitors and use a 0.047µF capacitor for the time constant.
In any given design, you may have an Arduino pin that is continuously being clocked at a relatively high frequency which you could use to drive the "pump".