Choosing Fish
The first thing you're going to want to do is decide what kinds of fish you're going to be keeping. You don't have to think about specifics right away, but choosing by group is going to benefit you in determining how the aquarium is set up so that you can have everything in place first before getting your fish in.
Just like with any other aquarium fish setup, you generally want to divide your choices by what layer of water they generally inhabit- topwater, mid-water, or bottom. If you're keeping a community, evening it out amongst the three is a good choice. Species aquariums, where only one species or one kind of fish is kept, can be geared more toward what that kind of fish wants. Here are some general fish hangouts:
Top- Topminnows, killifish, Gar
Middle- Shiners, Dace, Sunfish/Basses, chubs, fathead minnows
Bottom- Catfish, suckers, stonerollers, darters, perches, pickerel (mid/bottom), sculpins
Tank Size/ Dimension
As with most setups, bigger is better. Especially with minnows that like to be kept in groups, and sunfish that are more territorial. Some fish are perfectly fine in small aquaria.
Typically, you want to think about where you're finding your fish. If they're coming from a fast moving stream, you don't want a really tall aquarium where there will be little water movement toward the bottom. On the other hand, fish from a local retention pond that are used to floating casually won't appreciate a 1200 gph power head blowing at their face.
For fish that like ponds, a standard box aquarium is just fine, with no special requirements for flow. For river fish, they'll want that water moving, so longer tanks will do better. Of course, that doesn't mean it's impossible to keep, say, fast current darters in a standard 30g tall, but it's not preferred. Some fish though, may decline over time if the right situation isn't provided.
My personal set up is a 120g, 6' long. The minnows have lots of swimming space, and smaller fish have the room to get away from more aggressive fish. With the bigger space, I'm also able to provide different types of current to different areas of the tank, so slower fish can have some slack areas, and the fastest water can be directed to the front and middle where most of the shiners like to be.
Filtration
Most of our natives want clean water. Some will be more tolerant than others, but all will prefer a clear, well oxygenated aquarium with regular water changes provided.
For sunfishes, anything under the gravel is out. They're similar to keeping cichlids, and they like to dig. Stonerollers too, will dig pits in the substrate when they spawn. Under gravel filters use the gravel itself as the filter medium, so uncovering the plate renders the filter useless.
Most conventional filtration will work. For sunfish and larger fishes that make more waste, strong mechanical filtration with good biological filtration will be desired. The size and type really depends on the aquarium size. Large aquaria almost require a sump of some sort. For smaller aquaria, canister filters and hang on back filters will work just fine.
For fast moving water, you'll want to make sure the intake/ output of the filters are on opposite ends of the aquarium, so the water has a current. For long, large aquaria, extra power heads can be added throughout to make sure that water is really moving and to avoid dead spots where detritus can build up near the intake end. It also provides an opportunity to add more mechanical filtration via the powerhead intake.
In my setup, I have very little filtration. My aquarium is planted, and most of the detritus is allowed to deteriorate on the bottom to provide nutrients for the plants. Fish waste is essentially fertilizer. What I do have is a DIY internal canister. I built an acrylic tower from pieces of plexiglass, and inside is an 800gph pond pump. The tower is filled with a few dish scrubbers for bio filtration, a layer of white floss for fine mechanical filtration, and topped with standard blue filter padding for larger particles. I also have two powerheads placed along the back of the aquarium to provide added flow. With this setup, I do little to no water changes. Most waste product is used up by the plants. I have a little bio filtration to make up for what the plants don't use. Since it's a low tech (non- CO2) aquarium, any build up of fertilizer can be allowed to dissipate by halting fertilizer dosing for a couple weeks.
Substrate
Once again, think about where you're catching the fish. Rocky? Sandy? Silty? Regular aquarium gravel will work for most fish.
Some fish absolutely want sand- filter feeding fish like suckers. Suckers, like corydoras catfish and earth-eater cichlids, sift sand through their gills. Without a sandy substrate, they're relegated to eating in ways they're not used to.
Larger rocks should be provided for rocky stream fish. The minnows will use them as current breaks, and perching fish like darters will use them to hide in or sit on. Since my aquarium is planted, I had removed most of my rocks. When I added darters, I found that they hid all the time, I could hardly ever see them. By adding a couple small rocks to the foreground, the darters were encouraged to come out and now play king of the hill all day long.
There are some things to be avoided. Sharp, jagged rocks can cause damage to fast moving fish or fish with long fins. Rocks also should be figured into the water parameters. If your water is extremely hard, go add all the limestone you want. However, fish from a planty pond won't like that. Rocks with geodes or crystals should be avoided.
When using sand and gravel, particle size should be paid attention to. If it's too fine, detritus can build up on the surface and not sink down into the substrate to be broken down by aerobic bacteria in the top layers of the sand. Too much fine sand can also cause anaerobic pockets to form. This can cause harmful chemicals such as SO4 to build up, and can rot plant roots and poison fish.
If the particles are too large, food, poop, leaves, even dead fish can sink down into the cracks and rot, causing ammonia spikes. I personally advise against using pea gravel for this very reason, though some disagree with me.
Plants
Plants can be used very effectively in a native tank, so long as a few considerations are kept.
The first thing is deciding what kind of tank to keep- CO2 or low tech. If low tech, and you plan on using dirt as a substrate, digging fish are out. They'll make an absolute mess.
For digging fish without a dirt substrate, one option is to use something to protect the plant's roots from digging activities. One way to do that is by planting near rocks, or in crevices between rock groupings. Another way is to use fluorescent lighting grating. They come in 2' x 4' sheets at most hardware stores. By planting the roots into the grating, fish can't dig up plants without digging up the whole grating too. This is usually added when first setting up a tank, so may not be feasible for mature systems.
Current is a factor with some plants. Some plants do not want to be bent over all the time. Some don't mind it. Vallisneria is a good choice for tanks with moderate current. They will lay down in the water and have large roots that will anchor in well. Large plants that can rise above the current are good choices too, like certain types if ovular leaved Amazon swords. Leafy plants work well as a current buffer on the intake side of the aquarium, to keep the water from bouncing back and creating a swirling effect; however when placed near the output they will eventually decline as most do not like to be bent over in the current.
I would suggest using non-collected plants. Tropical plants, or other plants that are common in aquarium stores, are usually pretty consistent as to what they do and when. Natives though, can react to changes in the water associated with seasonal weather changes. A cold period in an unheated aquarium planted with Cabomba may cause the plant to brown out and lose it's needles as it would in fall in the wild. That makes for a nice mess, and most likely, the death of the plant. If you're trying for breeding fish, plants are probably out altogether since most native fish need their water to be brought down to at or near the 40s to trigger breeding.
I think I've covered most of it, if you have any suggestions, feel free to comment!
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