I would be very suspicious about it going stagnant.
You could fill it and begin the fishless cycle. The water circulation will help.
When you are ready to plant, drain it, keeping the filter running on a container of water, or open the filter and put the media in a bucket of water from the tank.
When you refill, dose the ammonia to only 1 ppm (many plants do not like ammonia too high) to finish out the cycle.
Here is the fishless cycle:
Cycle: To grow the beneficial bacteria that remove ammonia and nitrite from the aquarium.
Fish-In Cycle: To expose fish to toxins while using them as the source of ammonia to grow nitrogen cycle bacteria. Exposure to ammonia burns the gills and other soft tissue, stresses the fish and lowers their immunity. Exposure to nitrite makes the blood unable to carry oxygen. Research methemglobinemia for details.
Fishless Cycle: The safe way to grow more bacteria, faster, in an aquarium, pond or riparium.
The method I give here was developed by 2 scientists who wanted to quickly grow enough bacteria to fully stock a tank all at one time, with no plants helping, and overstock it as is common with Rift Lake Cichlid tanks.
1a) Set up the tank and all the equipment. You can plant if you want. Include the proper dose of dechlorinator with the water.
Optimum water chemistry:
GH and KH above 3 German degrees of hardness. A lot harder is just fine.
pH above 7, and into the mid 8s is just fine.
Temperature in the upper 70s F (mid 20s C) is good. Higher is OK if the water is well aerated.
A trace of other minerals may help. Usually this comes in with the water, but if you have a pinch of KH2PO4, that may be helpful.
High oxygen level. Make sure the filter and power heads are running well. Plenty of water circulation.
No toxins in the tank. If you washed the tank, or any part of the system with any sort of cleanser, soap, detergent, bleach or anything else make sure it is well rinsed. Do not put your hands in the tank when you are wearing any sort of cosmetics, perfume or hand lotion. No fish medicines of any sort.
A trace of salt (sodium chloride) is OK, but not required.
This method of growing bacteria will work in a marine system, too. The species of bacteria are different.
1b) Optional: Add any source of the bacteria that you are growing to seed the tank. Cycled media from a healthy tank is good. Decor or some gravel from a cycled tank is OK. Live plants or plastic are OK. I have even heard of the right bacteria growing in the bio film found on driftwood. (So if you have been soaking some driftwood in preparation to adding it to the tank, go ahead and put it into the tank) Bottled bacteria is great, but only if it contains Nitrospira species of bacteria. Read the label and do not waste your money on anything else.
At the time this was written the right species could be found in:
Dr. Tims One and Only
Tetra Safe Start
Microbe Lift Nite Out II
...and perhaps others.
You do not have to jump start the cycle. The right species of bacteria are all around, and will find the tank pretty fast.
2) Add ammonia until the test reads 5 ppm. This ammonia is the cheapest you can find. No surfactants, no perfumes. Read the fine print. This is often found at discount stores like Dollar Tree, or hardware stores like Ace. You could also use a dead shrimp form the grocery store, or fish food. Protein breaks down to become ammonia. You do not have good control over the ammonia level, though.
Some substrates release ammonia when they are submerged for the first time. Monitor the level and do enough water changes to keep the ammonia at the levels detailed below.
3) Test daily. For the first few days not much will happen, but the bacteria that remove ammonia are getting started. Finally the ammonia starts to drop. Add a little more, once a day, to test 5 ppm.
4) Test for nitrite. A day or so after the ammonia starts to drop the nitrite will show up. When it does allow the ammonia to drop to 3 ppm.
5) Test daily. Add ammonia to 3 ppm once a day. If the nitrite or ammonia go to 5 ppm do a water change to get these lower. The ammonia removing species and the nitrite removing species (Nitrospira) do not do well when the ammonia or nitrite are over 5 ppm.
6) When the ammonia and nitrite both hit zero 24 hours after you have added the ammonia the cycle is done. You can challenge the bacteria by adding a bit more than 3 ppm ammonia, and it should be able to handle that, too, within 24 hours.
7) Now test the nitrate. Probably sky high!
Do as big a water change as needed to lower the nitrate until it is safe for fish. Certainly well under 20, and a lot lower is better. This may call for more than one water change, and up to 100% water change is not a problem. Remember the dechlor!
If you will be stocking right away (within 24 hours) no need to add more ammonia. If stocking will be delayed keep feeding the bacteria by adding ammonia to 3 ppm once a day. You will need to do another water change right before adding the fish.
A) You can run a fishless cycle in a bucket to grow bacteria on almost any filter media like bio balls, sponges, ceramic bio noodles, lava rock or Matala mats. Simply set up any sort of water circulation such as a fountain pump or air bubbler and add the media to the bucket. Follow the directions for the fishless cycle. When the cycle is done add the media to the filter. I have run a canister filter in a bucket and done the fishless cycle.
B) The nitrogen cycle bacteria will live under a wide range of conditions and bounce back from minor set backs. By following the set up suggestions in part 1a) you are setting up optimum conditions for fastest reproduction and growth.
GH and KH can be as low as 1 degree, but watch it! These bacteria use the carbon in carbonates, and if it is all used up (KH = 0) the bacteria may die off.
pH as low as 6.5 is OK, but by 6.0 the bacteria are not going to be doing very well. They are still there, and will recover pretty well when conditions get better.
Temperature almost to freezing is OK, but they must not freeze, and they are not very active at all. They do survive in a pond, but they are slow to warm up and get going in the spring. This is where you might need to grow some in a bucket in a warm place and supplement the pond population. Too warm is not good, either. Tropical or room temperature tank temperatures are best. (68 to 85*F or 20 to 28*C)
Moderate oxygen can be tolerated for a while. However, to remove lots of ammonia and nitrite these bacteria must have oxygen. They turn one into the other by adding oxygen. If you must stop running the filter for an hour or so, no problem. If longer, remove the media and keep it where it will get more oxygen.
Once the bacteria are established they can tolerate some fish medicines. This is because they live in a complex film called Bio film on all the surfaces in the filter and the tank. Medicines do not enter the bio film well.
These bacteria do not need to live under water. They do just fine in a humid location. They live in healthy garden soil, as well as wet locations.
C) Planted tanks may not tolerate 3 ppm or 5 ppm ammonia. It is possible to cycle the tank at lower levels of ammonia so the plants do not get ammonia burn. Add ammonia to only 1 ppm, but test twice a day, and add ammonia as needed to keep it at 1 ppm. The plants are also part of the bio filter, and you may be able to add the fish sooner, if the plants are thriving.