Unless this will be a very large terrarium, you shouldn't need something as fancy as a Fluval for your filtration. Harmful bacteria should be taken care of by beneficial bacteria that will colonize the surfaces of your waterfeature, and never underestimate the ability of plants to purify water. Use live plants, not plastic ones! You could have a few aquatic plants, such as anubias, in the actual water area, and fill the land area with plants as well. Other than that, do regular partial water changes to get rid of the excess waste, and you shouldn't have any problems. You will need a pump to circulate the water, and most pumps have a sponge filter to prevent the pump from clogging. Just rinse this when you do your water changes (remember to use only distilled or RO water), and everything will be great. How big of a tank are you using?

I am in the process of building a large terrarium now. If you're willing to use wood, epoxy, and pondliner to make the tank, there's a way that you can use any filter your heart desires. My enclosure has a false bottom, however, drainage holes are drilled in the bottom of the cage. Using PVC tubing, water flows out of the cage (through the bottom) and into a tank under the cage, in which filters, heaters, ect. can be placed. A water pump takes the water from here and pumps it to the waterfall. This setup is originally hard to build, but later on, it makes water cahnges, filtering, and heating a breeze. Plus, its kinda fun to take on the challenge of building a tank from scratch. Just an idea though...it was actually conceived after I had built a 20 gallon terrarium for my gradis day gecko, and BTW, that has a waterfall and a false bottom but no filter at all and my gecko is happy and healthy.