an intermittent problem is usually electrical, or heat... I think most pond pumps and fish tank pumps have a thermal protector in line, that will reset itself when it cools, and would explain your problems... especially if it seems to be keeping time; more erratic timing I'd look electric side.
Is it really pumping water? Is it a submersible pump?
the pump motor, if submersible, is water cooled and needs to be underwater...
the pump itself is watercooled, and needs water flow to cool
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