Toxic contaminants. The effects of toxic contamination can be acute or chronic. Acute toxic effects are those that become manifest within forty-eight hours or so. Chronic, or long-term toxic effects are more insidious and can register as "diseases." Long-term toxicity can result in kidney and liver and spleen malfunctions eventually manifested as "bloat" and "dropsy" and in depression of the immune system, which subtly renders the fish vulnerable to pathogens.
Various forms of chemical filtration remove contaminants, including spent medication, from the water, before symptoms of distress appear. Your regimen of partial water changes dilute any toxins that may be present, but they don't eliminate them.
There are many sources of contaminants in aquarium water:
Household toxins. Indoor pollution can be unexpectedly high, the E.P.A. tells us, especially inside modern, energy-efficient, airtight home construction. I saw on the Web some time ago that elevated CO2 levels in tightly-enclosed living spaces were thought to be depressing the pH levels in some marine reef aquaria; when windows were opened a crack, pH levels rose. I'm not sure that I credit this tale without reservation, but it carries a good point.
Even if you methodically scrub the lotions and scents from your hands and arms and rinse off the soap residue every time you are going to dip them into an aquarium, indoor toxins abound, merely settling out of your air: substances released by incomplete combustion in heating and cooking, the ubiquitous perfumes and deodorizers in consumer goods and air-"fresheners," and their aerosol propellants themselves, fumes from household cleaning agents, solvents and unaired dry-cleaning, spray-painting done in a distant room, even decorating materials (remember "toxic carpet shock?"), though tobacco smoke is no longer so common, of course — all these can be more concentrated within the home than anything you'd be likely to encounter outdoors.
These pollutants are found in aerosol droplets that settle onto the water surface, or they bind to household dust, which gets into the aquarium system. Aerosol sprays can drift from room to room. If you need to control roaches, for instance, baited traps are safer for you and your family and for the fish. How many aerosol cans are there under your sinks, in your bathroom, in the cleaning closet? Are you still using hair spray?
Plant weights used to be made of uncoated bendable lead strips; I found a forgotten one left behind in substrate recently, now covered with white oxide in my acidic water: really that can't be good.
Plastics are tough and cheap, and they can be made more transparent even than glass. Though plastics are used everywhere in aquaria, lately there have been doubts about the softening compounds added to some plastics to keep them flexible. Flexible plastic can leach minute amounts of toxic chemicals like adipates and phthalates, which are suspected endocrine disrupters.
Pesticides are extremely poisonous to fish, even in trace amounts, as you know. Insecticides are commonly based on paralytic nerve poisons that are lethal to fishes in concentrations as low as one part in ten million, that is 0.1 ppm. Rotenone-based bug sprays are touted as "safe" for humans and our pet mammals, but rotenone is deadly to fish. Symptoms of poisoning include lack of coordination (watch the fish as they attempt to snap at food), staggering and spasms, panicky darting around, convulsions and loss of equilibrium. Subclinical levels may produce subtle, long-term effects.
One advantageous technology to keep in mind, the American Lung Association says, is a High Efficiency Particulate Arresting (HEPA) filter, such as you find increasingly on the better kinds of vacuum cleaners and air conditioners.
Nitrite toxicity. Not all toxicity comes from outside the aquarium. Nitrite is formed from ammonia by bacterial action, as you know, part of the nitrogen cycle. And you know that nitrite is toxic. Fish that are stricken with nitrite poisoning get lethargic. With higher levels they may gasp as if they were suffocating and die with their gillcovers open wide. The gills may be brownish rather than healthy pinkish-red.
Chloride reduces nitrite toxicity. Though the main effect of nitrite is on the oxygen-carrying component of red blood cells, in 2002 it was shown (in a paper read by O.T. Ferreira da Costa and M. N. Fernandes of the University of Saõ Carlos, Brazil, "Chloride cell changes induced by nitrite exposure...") to suppress chloride cells in the gill lamellae, which play a major role in maintaining a balance of salts in fish blood and organs. A small amount of chloride in the water will successfully compete with the nitrite for uptake, sparing the fish some of the nitrite toxicity. Salt (sodium chloride) is always what is recommended, but, since it's the chloride ion that is effective, you could use potassium chloride instead of sodium chloride. Plants will benefit from the potassium. Of course, this is a short-term, emergency measure: even a detectable trace of nitrite is an urgent signal that fundamental conditions are going wrong.