Impervious surfaces (roads, parking lots and sidewalks) are constructed during land development. During rain storms and other precipitation events, these surfaces (built from materials such as asphalt, cement, and concrete), along with rooftops, carry polluted stormwater to storm drains, instead of allowing the water to percolate through soil. This causes lowering of the water table (because groundwater recharge is lessened) and flooding since the amount of water that remains on the surface is greater. Most municipal storm sewer systems discharge stormwater, untreated, to streams, rivers and bays.
Water running off these impervious surfaces tends to pick up gasoline, motor oil, heavy metals, trash and other pollutants from roadways and parking lots, as well as fertilizers and pesticides from lawns. Roads and parking lots are major sources of polycyclic aromatic hydrocarbons (PAHs), which are created as combustion byproducts of gasoline and other fossil fuels, as well as of the heavy metals nickel, copper, zinc, cadmium, and lead. Roof runoff contributes high levels of synthetic organic compounds and zinc (from galvanized gutters). Fertilizer use on residental lawns, parks and golf courses is a significant source of nitrates and phosphorus.
As stormwater is channeled into storm drains and surface waters, the natural sediment load discharged to receiving waters decreases, but the water flow and velocity increases. In fact, the impervious cover in a typical city creates five times the runoff of a typical woodland of the same size.
...further declines in water quality remain likely if the land-use changes that typify more diffuse sources of pollution are not addressed... These include land-disturbing agricultural, silvicultural, urban, industrial, and construction activities from which hard-to-monitor pollutants emerge during wet-weather events. Pollution from these landscapes has been almost universally acknowledged as the most pressing challenge to the restoration of waterbodies and aquatic ecosystems nationwide. -National Research Council|Urban Stormwater Management in the United States 
The runoff also increases temperatures in streams, harming fish and other organisms. (A sudden burst of runoff from a rainstorm can cause a fish-killing shock of hot water.) Also, road salt used to melt snow on sidewalks and roadways can contaminate streams and groundwater aquifers.
One of the most pronounced effects of urban runoff is on watercourses that historically contained little or no water during dry weather periods (often called ephemeral streams.) When an area around such a stream is urbanized, the resultant runoff creates an unnatural year-round streamflow that hurts the vegetation, wildlife and stream bed of the waterway. Containing little or no sediment relative to the historic ratio of sediment to water, urban runoff rushes down the stream channel, ruining natural features such as meanders and sandbars, and creates severe erosion--increasing sediment loads at the mouth while severely incising the stream bed upstream. As an example, on many Southern California beaches at the mouth of a waterway, urban runoff carries trash, pollutants, excessive silt, and other wastes, and can pose moderate to severe health hazards.
Because of fertilizer and organic waste that urban runoff often carries, eutrophication often occurs in waterways affected by this type of runoff. After heavy rains, organic matter in the waterway is relatively high compared with natural levels, spurring growth of algae blooms that soon use up most of the oxygen. Once the naturally occurring oxygen in the water is depleted, the algae blooms die, and in their decomposing process, cause further eutrophication. Algae blooms mostly occur in areas with still water, such as stream pools and the pools behind dams, weirs, and some drop structures. Eutrophication usually comes with deadly consequences for fish and other aquatic organisms.
Excessive stream bank erosion may cause flooding and property damage. For many years governments have often responded to urban stream erosion problems by modifying the streams through construction of hardened embankments and similar control structures using concrete and masonry materials. Use of these hard materials destroys habitat for fish and other animals. Such a project may stabilize the immediate area where flood damage occurred, but often it simply shifts the problem to an upstream or downstream segment of the stream. See River engineering.
Effective control of urban runoff involves reducing the velocity and flow of stormwater, as well as reducing pollutant discharges. A variety of stormwater management practices and systems may be used to reduce the effects of urban runoff. Some of these techniques, called best management practices (BMPs) in the U.S., focus on water quantity control, while others focus on improving water quality, and some perform both functions.
Pollution prevention practices include low impact development techniques, installation of green roofs and improved chemical handling (e.g. management of motor fuels & oil, fertilizers and pesticides). Runoff mitigation systems include infiltration basins, bioretention systems, constructed wetlands, retention basins and similar devices.