Dead zones are generally caused by significant nutrient pollution, and are primarily a problem for bays, lakes and coastal waters since they receive excess nutrients from upstream sources. Excess nitrogen and phosphorus cause an overgrowth of algae in a short period of time, also called algae blooms.

A "dead lake" is a water body that can no longer support complex aquatic life, and the most common scientific cause is eutrophication. This process begins when an excess of nutrients, primarily nitrogen and phosphorus from agricultural runoff, sewage, or industrial waste, enters the water. These nutrients act as fertilizer, triggering massive algal blooms that blanket the surface and block sunlight from reaching underwater plants. When the algae eventually die and sink, the decomposition process performed by bacteria consumes the majority of the lake's dissolved oxygen, leading to hypoxia (low oxygen) or anoxia (no oxygen). Without enough oxygen, fish and other aerobic organisms suffocate, leaving behind a stagnant environment where only specialized anaerobic bacteria can survive. Other factors that can "kill" a lake include extreme acidification from acid rain, the introduction of toxic heavy metals, or severe salinity changes that disrupt the delicate osmotic balance required for native freshwater species to thrive and reproduce.