Yes! However, forming ice may cause flowing water to divert from its natural path, and may cause flooding or seepage. Additionally, keeping water moving from your pond through a fountain will reduce its ambient temperature as warmer water near the bottom is pumped up to the surface and exposed to the air. Keep this in mind while deciding whether or not to keep your waterfall going all winter.
Most pumps will have a minimum operating temperature listed in their user manual or on their manufacturer's website. Use this number as a guide for when its time to move your pump inside.
