I would say the skimmer is not a problem but the filter may be, what is in it? If you have a sponge or any other filter media at all I would say you are probably not doing the bacteria living (and dying) in that filter any favours. Those bacteria need oxygenated water and by turning your pump off at night the bacteria suffocates. I've read that it will start to suffocate with in 30 minutes. What makes the pump loud is it the sound of the water running, have you tried raising your water level? If it is the filter itself (motor) then I would suggest you replace it or service it. Most filters should be reasonably quiet in my opinion.
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