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.

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 include acidity (change in pH), electrical conductivity, temperature, and eutrophication. Eutrophication is the fertilization of surface water by nutrients that were previously scarce.

Water samples may be examined using the principles of analytical chemistry. Many published test methods are available for both organic and inorganic compounds. Frequently-used methods include pH, biochemical oxygen demand (BOD), chemical oxygen demand (COD), nutrients (nitrate and phosphorus compounds), metals (including copper, zinc, cadmium, lead and mercury), oil and grease, total petroleum hydrocarbons (TPH), and pesticides.

Source: Wikipedia (All text is available under the terms of the GNU Free Documentation License)

For more information (background, pictures, experiments and references): Water Pollution