Since 1962, Lake Whatcom's water quality has been monitored by staff from Whatcom County, the City of Bellingham, and Western Washington University's Institute for Watershed Studies.  In recent decades, the water quality in Lake Whatcom has been deteriorating due to increased phosphorus inputs that are resulting in algal blooms and depleted dissolved oxygen levels.  In 1998, Lake Whatcom was placed on Washington's list of polluted waters because it no longer met the state's dissolved oxygen level requirements.  Today, the City, County, and Lake Whatcom Water and Sewer District are working together with the Washington State Department of Ecology to create a plan to meet water quality standards.  In the meantime, Lake Whatcom is also vulnerable to many additional threats that are outlined below.
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Stormwater runoff — water from rainfall or snowmelt that moves over the ground — is the most common cause of water pollution. When stormwater picks up fertilizer, pesticides, oil, soap, and bacteria from pet waste, it can pollute our local waters.
Nutrients, such as phosphorus, are essential elements organisms need to live, grow, and reproduce. When found in large quantities, nutrients can be harmful to plants, animals, and water quality.   Excessive amounts of phosphorus has led to explosive algae growth and depleted dissolved oxygen levels in Lake Whatcom. 
Bacteria are microscopic, unicellular organisms that divide through cell division. Fecal coliform bacteria are associated with waste from humans and other warm-blooded animals. When found in high concentrations in water samples, Fecal coliform can indicate the presence of other disease-causing microorganisms.
Aquatic invasive species are non-native aquatic plants, animals, and pathogens that thrive in new environments and can cause economic loss, environmental damage, and harm to human health.  These species can end up in our lakes and streams by attaching themselves to boats, recreational equipment, and field gear.
Heavy metals can be found naturally in our environment, but in concentrated quantities they can adversely affect water quality, be toxic to aquatic life, and cause human health concerns. 
Hydrocarbons such as oil, gas, and grease, are organic compounds that are made up of carbon-hydrogen bonds. Some hydrocarbon pollutants can result in negative health impacts to humans and wildlife.
Pesticides are substances that are intended to prevent, destroy, repel, or mitigate, such as insecticides, herbicides, and fungicides. When pesticides end up in our lakes and streams, they threaten aquatic life and can impact our drinking water quality.
Climate Change refers to changes in long-term trends in the average climate. Projected changes in temperature and precipitation may result in impacts to Lake Whatcom's water quality and quantity due to reduced snowpack levels, changes in water temperature, and altered timing and amount of stream flows.