DIY Watering - Required components
I have some details about running motors etc. from Arduino pins at Driving motors, lights, etc. from an Arduino output pin.

Quite possibly what would work for you is a MOSFET - as Majenko suggested - connected up like this:



In this case you connect the positive side of your 12V supply for your pump to the pump, and the MOSFET sinks current to ground, when you require the pump on.

Don't forget the diode D1 which prevents damage from the inductive load of the pump generating high-voltage spikes.