Here's the part on Chlorination from the paper...
The Risks of Chlorination
Chlorine is an element widely used in modern chemistry be cause it readily reacts with so many substances. The vast majority of public water systems in this country use chlorine to disinfect their drinking water. But the widespread application of chlorine as a drinking water disinfecting agent has raised concerns about the risk of human exposure to chlorine and its by-products. Past experience with chlorine based compounds such as DDT, PCBs, and CFCs, which were later found to pose risks to health and the environment, have encouraged some environmental groups to call for a total ban on all uses of chlorine, rather than waiting to study each use of chlorine and its potential alternatives (Amato 1993).
Chlorine is toxic not just to microbes but to humans as well. Chlorine gas escaping at the treatment plant can cause acute health effects in workers, since the chemical is highly irritant to the eyes, nasal passages, and respiratory system. Inhalation of the gas can prove fatal at concentrations as low as 0.1% by volume (1,000 ppm) (AWWA 1984). At the minute amounts used in drinking water, however, the acute toxicity of chlorine is quite low. It is rather the potential long term risk of cancer from chronic exposure to moderate amounts of chlorine that is the major concern with the chemical in the drinking water supply. Much of the cancer risk from chlorine stems from the class of complex chloroorganic compounds, known as trihalomethanes (THMs), that are formed as one of the major by products of the chlorination process. Trihalomethanes are formed when chlorine is added to water containing organic materials, such as the humic and fulvic acids emitted from decomposing plant and animal materials in the water supply (Rook 1974; Bellar et al. 1974). Although THMs occur with chlorination of both surface and ground waters, their concentration is much greater with surface water because of its higher levels of naturally occurring organic materials.
Of particular concern among the THMs is chloroform, the most prevalent and thoroughly studied member of the THM group. Ingestion of chloroform has been associated with an increased incidence of cancerous tumors in multiple laboratory animal bioassays. These tumors occurred at several sites, most notably in the kidney and liver, as well as across several different species and strains of animals (National Cancer Institute 1976; Roe et al. 1979) (see Table 7.1). Although many of the animal studies focused on chloroform administered in corn oil or toothpaste, others also found increased evidence of tumors when the chloroform was administered in drinking water (Jorgenson et al. 1985).
Using the mouse liver tumor data (NCI 1976), the EPA originally estimated an upper-bound cancer risk--that is, a worst-case analysis--that indicated that the lifetime risk from exposure to chloroform could reach as high as one cancer per 2,500 members of the population exposed (EPA 1977). On the basis of this analysis, the agency began to regulate chloroform and other THMs in 1979, setting a "maximum contaminant level" of 0.10 milligrams per liter (or 100 parts per billion) for total trihalomethanes in the drinking water supply. The incremental lifetime cancer risk from ingesting chloroform in household water at this level has been estimated to be about two in 100,000 (Maxwell et al. 1991). In other words, if 200 million people drank household water at EPA's maximum chloroform level for their entire lives, about 4,000 would die of chloroform induced cancer.
Chloroform is not the only by-product formed in the chlorination process that has been subjected to animal toxicity testing. Other major trihalomethanes, as well as trichloroacetic acid, dichloroacetic acid, various haloacetonitriles, and chlorophenols have been reported to show carcinogenicity, mutagenicity, or other toxic properties (Cotruvo and Regelski 1989; Simmon and Tardiff 1978; Herren-Freund et al. 1987; Bull 1982). For other by-products, however, such as various chlorinated acids, alcohols, aldehydes, and ketones, there is limited information on their potential toxic effects (Cotruvo and Regelski 1989). There is also a plethora of nonvolatile byproducts formed in the chlorination process for which there are limited data on toxicity and other effects (NAS 1987). Identifying and testing these substances has been a relatively slow process, and much work is continuing in this area (Bull 1982).
In humans, chlorinated water has been associated with an increased risk of bladder, colon, and rectal cancer in multiple epidemiological studies (Crump and Guess 1982; Williamson 1981). These studies, in general, have found the risks of bladder, colon, and rectal cancer associated with drinking chlorinated water to be about 1.1 to 2.0 times higher than the risk for drinking the same quantity of unchlorinated water (Crump and Guess 1982). The aggregate cancer risk from drinking chlorinated water over a lifetime, however, remains modest.
One of the studies finding a significant positive association, the large case control work by Cantor and colleagues (1987), suggests that lifetime consumption of chlorinated water in creases the risk of bladder cancer by a factor of about two. The study compared those residing for more than forty years in communities where drinking water was chlorinated with those who drink unchlorinated water. This association may result in about 1,000 to 3,000 excess bladder cancers per year in the United States and could explain as much as 25 to 30 percent of the occurrence of bladder cancer in adults residing in chlorinated communities (Cantor et al. 1987).
As with many epidemiological studies, however, there are numerous problems with the studies of chlorinated water. Multiple uncontrolled confounding factors (for example, smoking, diet, occupation, lifestyle) could also explain part or all of the observed cancer rates. Inexactness in measuring the chlorine level, water consumption, population migration, and other variables detracts from the definitiveness of the estimated association. Also, because much of the nation's water is chlorinated, the number of individuals who can serve as study controls those who drink unchlorinated water-is limited. Taken together, however, these studies have been interpreted as suggesting a significant association of bladder, colon, and rectal cancer with chlorinated drinking water (EPA 1985). This risk is highest in drinking water contaminated with organic material, but, given the myriad by-products formed in the chlorination process, any of a number of substances or combination of substances could be involved.
Additional health effects from chlorine have also been revealed in human studies. Of particular interest is a suggested relationship between consumption of chlorinated water and an increase in the total serum cholesterol levels of populations suffering from a diet deficient in calcium. While the increase in cholesterol levels was found to be small, it suggests that consumption of chlorinated water could be a possible risk factor for cardiovascular disease as well as for cancer (Wones et al. 1989; Zeighami et al. 1990).
Ingestion is not the only route of exposure to these substances in drinking water. There may also be adverse effects from inhalation or dermal exposure during showering, bathing, or swimming. It has been postulated, for example, that exposure to volatile chemicals in drinking water through inhalation may be as large or even larger than exposure from ingestion alone (Maxwell et al. 1991; McKone 1987).
As with most suspected carcinogens, the adverse health effects associated with chlorine by-products are largely chronic, cumulative, and may involve a long latency period before they appear. The health risks are estimated assuming a constant exposure of many years or often many decades. It may also be several decades before any adverse effects, such as excess cases of cancer, become apparent.