Your setup didn't fail because the pumps were cheap, it failed because 9V batteries are not suited for motors of any significant size. Here are the discharge curves for a few different brands of PP3 9V batteries under 1A loads:
Image source: PowerStream - Testing 9 Volt Batteries for mAH capacity and voltage sag during discharge
You can see that the voltage starts well below 9V and very quickly (within seconds) falls below 7V and hangs out around 5-6V before falling off a cliff after a few minutes - 4.2 minutes for the Duracell - when the battery is considered "dead". 9V batteries are very well for smoke detectors or remote controls where the current draw is measured in microamps or milliamps, but for pumps you will need something designed for high current instead of longevity.
As you can also see from the curves, the voltage is not constant over the discharge range so you will also need to figure out how you want to deliver a relatively constant 12V to your motors. This is fairly easily accomplished with a DC-DC converter that can also boost the battery voltage. Fully-integrated modules are available that require no extra parts, just be sure to size it appropriately for both the continuous current draw of your motor and the initial starting surge of up to 3x the continuous current.
The very popular 18650 lithium-ion batteries have capacities ~2000mAh, an order of magnitude higher than a 9V and can handle 1A discharge rates easily. Some of them have integrated charge circuitry or I would find a charging system compatible with your batteries. Purchasing bare cells is not worth your time or effort. Wall warts are another option if the device doesn't need to be portable.
