The Nitrogen Cycle Paradox

The nitrogen cycle is an important process in an aquatic ecosystem.
Nitrogen is used by plants, fish, and other aquatic organisms to produce a number of complex organic molecules like amino acids, proteins and nucleic acids. Animals receive the required nitrogen they need for metabolism, growth, and reproduction by the consumption of living or dead organic matter containing molecules composed partially of nitrogen. Aquatic plants such as algae receive the nitrogen primarily from the nitrates in the water.
In a closed aquatic system such as a garden pond or water garden, the store of nitrogen is primarily stored in living and dead organic matter such as fish food, dead leaves, rotting algae, fish waste, etc.

Fish and other aquatic animals can excrete ammonia directly in the water.
Ammonia is also created through rotten leaves and vegetation and sludge.
Ammonia is extremely toxic and even relatively low levels pose a threat to fish health.
Ammonia is chemically converted into nitrite (NO2-) by Nitrosomonas.
Further modification from the nitrite to nitrate (NO3- ) is process by Nitrobacter (another bacteria).
The chemical oxidation processes of converting ammonia to nitrite and nitrite to nitrate are known as nitrification.
Nitrate is often perceived to be the safe end-point of the Nitrogen Cycle.
Nitrate is very soluble and it is easily absorbed by algae in the water causing blooms of green water.

Nitrifying bacteria usually take several months to slowly reestablish every Spring and in new ponds before the Nitrogen Cycle can be established. Cycling also occurs when pond condition changes such as adding new fish.
When Nitrogen Cycle does not work correctly, your pond will quickly turn into a foul smelling and deadly sewage mess.
However, when the nitrification process is working and all the nitrifying bacteria are working, more nitrate is produced.
Nitrate is the primary nutrient for algae to grow.
In a closed pond system, absorption by algae is the only way to remove excess nitrates.
As a result, the water turns green and you will not see the fish..
The paradox is when Nitrogen Cycle works well, the pond is full of algae and turns green.
Although this is a normal process, it is aesthetically not pleasing to the pond owner.
More algae also removes more oxygen during the night when the algae undergoes respiration (oxygen capturing) instead of photosynthesis (oxygen producing).
Fish and beneficial bacteria starve of oxygen during the nights in an algae filled pond.
At the critical limit, fish and beneficial bacteria will start to die.
Your established filtration system will lose its ability as a bio-filter and the nitrification process stops working.
Living organisms will continue to die back to where the ecosystem balances itself again and for the nitrogen cycle to reestablish.