The principal environmental issues associated with runoff are the impacts to surface water, groundwater and soil through transport of water pollutants to these systems. Ultimately these consequences translate into human health risk, ecosystem disturbance and aesthetic impact to water resources. Some of the contaminants that create the greatest impact to surface waters arising from runoff are petroleum substances, herbicides and fertilizers. Quantitative uptake by surface runoff of pesticides and other contaminants has been studied since the 1960s, and early on contact of pesticides with water was known to enhance phytotoxicity.  In the case of surface waters, the impacts translate to water pollution, since the streams and rivers have received runoff carrying various chemicals or sediments. When surface waters are used as potable water supplies, they can be compromised regarding health risks and drinking water aesthetics (that is, odor, color and turbidity effects). Contaminated surface waters risk altering the metabolic processes of the aquatic species that they host; these alterations can lead to death, such as fish kills, or alter the balance of populations present. Other specific impacts are on animal mating, spawning, egg and larvae viability, juvenile survival and plant productivity.  Some research shows surface runoff of pesticides, such as DDT, can alter the gender of fish species genetically, which transforms male into female fish.
Surface runoff occurring within forests can supply lakes with high loads of mineral nitrogen and phosphorus leading to eutrophication. Runoff waters within coniferous forests are also enriched with humic acids and can lead to humification of water bodies  Additionally, high standing and young islands in the tropics and subtropics can undergo high soil erosion rates and also contribute large material fluxes to the coastal ocean. Such land derived runoff of sediment nutrients, carbon, and contaminants can have large impacts on global biogeochemical cycles and marine and coastal ecosystems.
In the case of groundwater, the main issue is contamination of drinking water, if the aquifer is abstracted for human use. Regarding soil contamination, runoff waters can have two important pathways of concern. Firstly, runoff water can extract soil contaminants and carry them in the form of water pollution to even more sensitive aquatic habitats. Secondly, runoff can deposit contaminants on pristine soils, creating health or ecological consequences.