The most difficult thing is making the correct diagnosis of what your fish has got.
Fish disease fall into a few main categories. There are a few exceptions but most fish health issues are caused by poor water quality, or the following pathogens.
Protozoan infections
Bacterial infections
Fungal infections
Parasitic worms and flukes.
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External protozoan infections are relatively easy to identify. They all cause fish to rub on objects. Things like white spot and velvet show up as white dots or a yellow/ gold sheen over the body and fins. Costia, Chilodonella & Trichodina cause fish to produce excess mucous over the infected area/s and it appears as cream, white or grey patches over the body.
Poor water quality will show up as a cream, white or grey film over the body and fins. With external protozoan infections like Costia, Chilodonella & Trichodina, the fish only get cream, white or grey patches where the parasites are eating the fish. Whereas poor water quality causes the fish to produce excess mucous all over its body and fins.
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Bacterial infections usually appear as red sores or inflamed areas. Sometimes with cream or white over them. The cream or white areas are excess mucous produced by the fish to protect the damaged area.
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Fungal infections
The most commonly seen fungal infection in fish is Saprolegnia and looks like white fluff sticking out from the body. Most fungal infections in fish occur in damaged/ open tissue or wounds. If the fish don't have any physical wounds, they are unlikely to get a Saprolegnia infection.
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Parasitic worms and flukes can be divided into two main groups. Intestinal worms and external flukes, which include gill flukes.
Intestinal worms usually cause fish to lose weight, but heavily infested fish can look fat like a pregnant guppy. If they have Camallanus or Capillaria thread worms, these can sometimes be seen hanging out the fish's butt and look like thin red or white hairs. Tapeworm just cause fish to lose weight over time (several months or more).
External flukes can usually be seen on the fish's body or fins.
Gill flukes will cause fish to breath heavily. Poor water quality and low oxygen levels do too. But if you test the water and it's good, and the tank and filter are clean, and there is plenty of aeration/ surface turbulence, then fish that are otherwise healthy but breathing more than normal, probably have gill flukes.
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There are a few other unusual diseases in fish including microsporidian and spironucleus infections, and black spot disease caused by parasitic worms from terrestrial animals. However, these aren't commonly seen in aquariums.
