Sewage
In developing countries, an estimated 90% of wastewater is discharged directly into rivers and streams without treatment. Even in modern countries, untreated sewage, poorly treated sewage, or overflow from under-capacity sewage treatment facilities can send disease-bearing water into rivers and oceans. In the US, 850 billion gallons of raw sewage are sent into US rivers, lakes, and bays every year by leaking sewer systems and inadequate combined sewer/storm systems that overflow during heavy rains. Leaking septic tanks and other sources of sewage can cause groundwater and stream contamination.
Beaches also suffer the effects of water pollution from sewage. The chart below shows the typical reasons that about 25% of the beaches in the US are put under water pollution advisories or are closed each year. It's clear that sewage is part of the problem, even in what is supposedly the most advanced country in the world.
Air Pollution
Hey, I thought we were doing WATER pollution causes! Well, surprisingly enough, air pollution contributes substantially to water pollution. Pollutants like mercury, sulfur dioxide, nitric oxides, and ammonia deposit out of the air and then cause problems like mercury contamination in fish, acidification of lakes, and eutrophication (nutrient pollution). Most of the air pollution that affects water comes from coal-fired power plants and the tailpipes of our vehicles, though some also comes from industrial emissions.
Carbon Dioxide
According to the United Nations Environment Programme, a 15-year-long study of the role of man-made CO2 in the earth's oceans found that the oceans had absorbed enough CO2 to already have caused a slight increase in ocean acidification. The fear is that further CO2 uptake will increase acidification even more and cause the carbonate structures of corals, algae, and marine plankton to dissolve. This could have significant impacts on the biological systems of our oceans.
Heat
Heat is a water pollutant—increased water temperatures result in the deaths of many aquatic organisms. These increases in temperature are most often caused by discharges of cooling water by factories and power plants.
Global warming is also imparting additional heat to the oceans. The impact on marine life is unknown at this point, but it's likely to be significant.
Noise
Many marine organisms, including marine mammals, sea turtles and fish, use sound to communicate, navigate, and hunt. The ever-increasing din of noise from ship engines and sonars has a negative effect. Because of this noise pollution, some species may have a harder time hunting; others may have a harder time detecting predators; still others may just not be able to navigate properly.
In a well publicized case in 2000, at least 17 whales were stranded on beaches in the northern Bahama Islands, with the likely cause being US Navy vessels operating mid-frequency sonar systems nearby.