If your pet water fountain comes with a filter, you shouldn’t use the fountain without a filter. The filter cleans the water and removes impurities that could damage the internal components and accumulate in the cracks and crevices. It also prevents contaminants from lingering in water that sits in the fountain for a long time. However, the fountain can run without the filter, and it’s better to remove the filter than to leave the old filter to accumulate bacteria if you never change it.