Organics build up in aquariums from uneaten food, fish excretions, decaying plant matter and from the remains of any dead livestock such as snails and fish.
The bacteria in your aquarium do a great job of converting organic waste into compounds plants can use, but they can’t process larger materials quickly enough before organics start releasing into the water column.
Manually removing waste by hand and siphon, performing weekly water changes and regular maintenance of your mechanical filtration goes a long way to keeping organics under control. You can also add livestock such as shrimp and snails to help break down decaying plants and uneaten food before they start to rot.
You should also ensure your filtration is adequate for the size of your tank and that water is circulating enough to move smaller waste into your filtration where the bacteria can do its job.
The last aspect to consider is the age of your aquarium. Newly set-up aquariums will still be “cycling” – that is, the process of your filter growing a bed of beneficial bacteria. At this early stage of your aquarium’s life, the filter doesn’t have sufficient bacteria to remove these organics.
This is often referred to as “new tank syndrome” and is simply a part of the process – once your aquarium has had time to cycle and establish its good bacteria, it should be much easier to achieve balance.
Keeping your aquarium densely planted from the start is also an excellent way to keep new tank syndrome under control as the plants work to consume ammonia and other compounds.