Took a group to BWCA in 2007. We had 3 Varios and 1 Hiker. All 3 of the Varios went south on us after about 10 gallons. Very disappointed. The water is crystal clear so that wasn't an issue.
The lake water in the BWCA looks clear, but that doesn't mean that there is nothing there to be filtered out. The ceramic filter cartridge (vario) pore size is smaller than the hiker's paper filter and will catch a lot of stuff (invisible, and nearly so, like some algaes) that the hiker will miss. There is nothing wrong with the varios in this respect.
If you want to keep the filter from clogging, especially later in the season when the organic matter concentration is higher, then you'll have to use a pre-filter. Best thing is to make you own from a section of a house water filter cartridge, some scrap acrylic sheet and a threaded barb fitting and put in on the intake tube of the filter. This will work for any water filter and will greatly extend the life of your main cartridge if you use a cartridge with a nominal pore size of 1 micron, like a CB2.
All that said, using a hiker with the paper cartridge or the vario on the high flow setting (i.e. going around the ceramic filter) should be good enough to avoid the beaver fever--which is not a huge problem in most of the lakes anyhow.
Just get your water well away from shore and preferably in a deep part of the lake avoiding areas with significant current. Giardia cysts are heavier than water and will settle to the bottom. If you are getting water from the shore, don't disturb the sediment on the bottom, it will have a relatively higher cyst concentration--if indeed the lake is contaminated. If you can collect the water from a foot or more below the surface, the better off you'll be; the farther down you go, the less algae there is.
I've been on over 25 extended trips to the BWCA and Canada and haven't been sick once including all the times when we used iodine and did not let it sit long enough before we drank the water...