The specific contaminants leading to pollution in water include a wide spectrum of chemicals, pathogens, and physical or sensory changes such as elevated temperature and discoloration. While many of the chemicals and substances that are regulated may be naturally occurring (calcium, sodium, iron, manganese, etc.) the concentration is often the key in determining what is a natural component of water, and what is a contaminant. High concentrations of naturally-occurring substances can have negative impacts on aquatic flora and fauna.
Oxygen-depleting substances may be natural materials, such as plant matter (e.g. leaves and grass) as well as man-made chemicals. Other natural and anthropogenic substances may cause turbidity (cloudiness) which blocks light and disrupts plant growth, and clogs the gills of some fish species.
Many of the chemical substances are toxic. Pathogens can produce waterborne diseases in either human or animal hosts. Alteration of water's physical chemistry includes acidity (change in pH), electrical conductivity, temperature, and eutrophication. Eutrophication is an increase in the concentration of chemical nutrients in an ecosystem to an extent that increases in the primary productivity of the ecosystem. Depending on the degree of eutrophication, subsequent negative environmental effects such as anoxia (oxygen depletion) and severe reductions in water quality may occur, affecting fish and other animal populations.
Pathogens

A manhole cover unable to contain a sanitary sewer overflow.
Coliform bacteria are a commonly used bacterial indicator of water pollution, although not an actual cause of disease. Other microorganisms sometimes found in surface waters which have caused human health problems include:
- Burkholderia pseudomallei
- Cryptosporidium parvum
- Giardia lamblia
- Salmonella
- Novovirus and other viruses
- Parasitic worms (helminths).
High levels of pathogens may result from inadequately treated sewage discharges. This can be caused by a sewage plant designed with less than secondary treatment(more typical in less-developed countries). In developed countries, older cities with aging infrastructure may have leaky sewage collection systems (pipes, pumps, valves), which can cause sanitary sewer overflows. Some cities also have combined sewers, which may discharge untreated sewage during rain storms.
Pathogen discharges may also be caused by poorly managed livestock operations.