JDA beat me to it...I'd say UV would be your best bet. There are a couple charts floating around that will tell you the amount of exposure needed to kill the algae/microfauna that you are targetting. You an reference that target level with the charts provided by the UV filter manufacturer to figure out the UV wattage and gph you'll need to run through it to reach your exposure level. I'll see if I can dig them up...
edit: found the 2 charts. This is for AquaUV sterilizers, but it should give you a decent idea...each company should have their own charts
and here's the exposure chart
Essentially, you'll want to have an exposure around 200k to sterilize the water.