I have it run in my system too. But beside killing bad algae, the UV also kill good algae as well. So I have it hooked up but I'm running it less now, I let it on more often if I have ich or algae outbreak. Especially if you're dosing microbacter7 or bacteria supplement then you'll need to turn it off before dosing and keep it turned off for 4 hours after dosing so the bacteria have more time to settle or attach to rock/sand and doesn't get killed by the UV.