All forms of chlorine are widely used, despite their respective drawbacks. One drawback is that chlorine from any source reacts with natural organic compounds in the water to form potentially harmful chemical by-products. These by-products, trihalomethanes (THMs) and haloacetic acids (HAAs), are both carcinogenic in large quantities and are regulated by the United States Environmental Protection Agency (EPA) and the Drinking Water Inspectorate in the UK. The formation of THMs and haloacetic acids may be minimized by effective removal of as many organics from the water as possible prior to chlorine addition. Although chlorine is effective in killing bacteria, it has limited effectiveness against pathogenic protozoa that form cysts in water such as Giardia lamblia and Cryptosporidium.

In some systems, the carbon prefilter is omitted, and a cellulose triacetate membrane is used. CTA (cellulose triacetate) is a paper by-product membrane bonded to a synthetic layer and is made to allow contact with chlorine in the water. These require a small amount of chlorine in the water source to prevent bacteria from forming on it. The typical rejection rate for CTA membranes is 85–95%.
The addition of inorganic coagulants such as aluminum sulfate (or alum) or iron (III) salts such as iron(III) chloride cause several simultaneous chemical and physical interactions on and among the particles. Within seconds, negative charges on the particles are neutralized by inorganic coagulants. Also within seconds, metal hydroxide precipitates of the iron and aluminium ions begin to form. These precipitates combine into larger particles under natural processes such as Brownian motion and through induced mixing which is sometimes referred to as flocculation. Amorphous metal hydroxides are known as "floc". Large, amorphous aluminum and iron (III) hydroxides adsorb and enmesh particles in suspension and facilitate the removal of particles by subsequent processes of sedimentation and filtration.[6]:8.2–8.3
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