The aquatic habitat alterations category includes a diverse group of stressors with various origins and impacts.
- Hypoxia (i.e., oxygen levels low enough to affect most organisms) occurs in the bottom waters of some highly productive regions of the Great Lakes during late summer.
- Ports and harbors concentrate shipping and other industrial activities in river mouths and embayments, with associated increased risk of physical habitat disturbance and pollutants.
- Light pollution due to human activity is especially pronounced in near shore areas of high population density.
- Marinas are another potential source of habitat disturbance and pollution due to heavy boat traffic, which can disturb physical habitat, and boat maintenance in poorly flushed water.
- Shipping lanes carry heavy ship traffic which may spill hazardous chemicals and create wave action in shallow or near shore areas.
- Shoreline hardening efforts including revetments, sea walls, rip-rap and other barriers to erosion alter near shore sediment dynamics and accelerate lakebed erosion, as do shoreline extensions such as piers and shore-normal breakwaters.
- Tributary dams can significantly affect Great Lakes migratory fish species, like lake sturgeon, by eliminating access to spawning habitat. Tributary dams may also affect habitats within the Lakes due to altered flow, sediment and nutrient regimes.