Chlorine is the chemical most often used to keep swimming pools and Jacuzzis free of bacteria that can be hazardous to humans.
Chlorine kills bacteria though a fairly simple chemical reaction. The chlorine solution you pour into the water breaks down into many different chemicals, including hypochlorous acid (HOCl) and hypochlorite ion (OCl-). Both kill microorganisms and bacteria by attacking the lipids in the cell walls and destroying the enzymes and structures inside the cell, rendering them oxidized and harmless. The difference between HOCl and OCl- is the speed at which they oxidize. Hypochlorous acid is able to oxidize the organisms in several seconds, while the hypochlorite ion may take up to 30 minutes.
The levels of HOCl and OCl- vary with the pool's pH level. If the pH is too high, not enough HOCl is present and pool cleaning can take much longer than normal. Ideally, the level of pH in the pool should be between 7 and 8; 7.4 is ideal -- this is the pH of human tears. Once the HOCl and OCl- are done cleaning the pool, they either combine with another chemical, such as ammonia, or are broken down into single atoms. Both of these processes render the chlorine harmless. Sunlight speeds these processes up. You have to keep adding chlorine to the pool as it breaks down.
While the bacteria-killing properties of chlorine are very useful, chlorine also has some side effects that can be annoying to humans, and possibly even hazardous. Chlorine has a very distinctive smell that most find unpleasant, and some find overwhelming. There is also the "itch factor" -- chlorine can cause certain skin types to become itchy and irritated. The hypochlorite ion causes many fabrics to fade quickly when not rinsed off immediately after exiting the pool. This is why your swimsuit looks faded and worn so early in the summer.
Extremely high amounts of chlorine gas hovering above your pool can be hazardous to your breathing. Some companies have developed alternatives to chlorine, including other chemicals and ion generators. Some of these are good alternatives, but they don't achieve the cleanliness, oxidation levels or low price that chlorine provides.
Here are some interesting links: