Is your barrier solid, or mesh? If it's solid, it wouldn't be able to filter the water on the other side of the barrier because the barrier is blocking the water on the side the filter isn't on. Does that make sense?
Hmm. How big is your tank? Maybe the filter's flow isn't strong enough to get the water on the other side of the barrier?
Ahaha I realized probably no barriers are sold solid because if you are using a filter the filter wouldn't be able to get to the water on the other side of the barrier. lol I feel stupid. =P
A lot of dividers are like this. The holes would have to be large for you to get a water flow through it. You may want to put another filter on the other side or just do water changes more often on the side with out the filter.
Could you put the filter so that the intake is on one side and the outflow is on the other? That's the only thing I can think of. It depends on what kind of filter you have though. Might not work for all.
if you have an undergravel filter you can cut out notches in the underplates connecting the 2 sides then the intake will pull water from both sides, however you can also connect a second filter flute and itll also keep the tank cleaner.
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