If you are worried about water quality you can always use a filter. I like to use an external canister filter. But for my small water features I don't bother with anything, the plants tend to keep things clean. When I fertilize I use a spray bottle and spray the plants I want to get fertilized, but I almost never do it when there are animals in the terrarium.
Also make sure you water with distilled or RO water before fertilizing otherwise things might get too salty for the roots to survive.
I only take out water when there is too much water, that is why I always make a water feature. My water features are basically depressions in the ground level that fill up with water, giving me access to the water. When there is too much water I simply take it out with a turkey baster or something.
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"We must not look at goblin men,
We must not buy their fruits:
Who knows upon what soil they fed
Their hungry thirsty roots?"
Goblin Market
by Christina Georgina Rossetti
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Keeping water fresh
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