Well, depending on the tank, load, and filter size, sometimes the gunk trapped in the filter media can get ahead of the bacteria's ability to break it down. It isn't an Eheim brand problem. It is an every filter problem.
If any filter gets gunked full of junk, you'll have decomposition and waste products being dissolved into the water column and circulated back into your open aquarium. Stuff trapped in your filter is still in your water column just like stuff floating around in your tank. It may be kept out of sight, but it is still decomposing in your water column.
The filter houses large bacterial colonies that break stuff down into less toxic components. Ammonia gets broken down to less toxic nitrite. Nitrite gets broken down to less toxic nitrate. (I originally had nitrite and nitrate transposed in this post. I edited this post to correct the mistake. The above breakdown is now correct.)
So, the bacteria in your aquarium help, but you can still get an accumulation of stuff that is too much for the bacteria to handle.
Filters have media inside that traps stuff. Now, that stuff does not magically disappear when it gets caught in the filter media. Filters are also designed so that you can get inside them and remove this media. There is a purpose for this. The filter collects gunk in one spot but it is still up to you to remove that collected gunk periodically. Finding the sweet spot in that maintenance schedule is up to the user.
"Insanity: doing [or asking] the same thing over and over again and expecting different results."
Last edited by random_alias; 11-30-2010 at 02:27 PM.