Poor Resource Management
Overexploited fish stocks and the declining abundance of marine species and their habitats are some symptoms of the ineffective management of human activities within the ecoregion. Destructive fishing activities that include bottom trawling continue to damage bottom habitats and have high levels of bycatch. Isolated sector-by-sector management approaches have failed to holistically consider the impacts of human activities on the ocean ecosystems and their functioning.

In addition, in B.C. the multiple federal and provincial jurisdictional issues in the marine environment and unresolved First Nation rights have meant there has been a lack of clarity on resource management mandates. This has significantly limited the progress on large area-based  planning measures.

The forest sector in B.C. has been heavily criticized for poor resource management practices in the past decades. Poor land management and forestry affects not only the forest habitats and species, but also the soils, the watersheds, and even downstream to the ocean. After years of conflict, a more holistic, ecosystem-based approach is emerging.

Marine Pollution and Invasive Species
A variety of forms of pollution pose threats to biodiversity in the Northeast Pacific ecoregion. Ship source pollution, including oil and fuel spills and bilge oil from marine vessels, affects a variety of seabird and marine species. Increased land-based activities and urban development have also resulted in pollution and a decline in water quality in localized areas.

Increased shipping activities have brought aquatic invasive species from foreign ports that are displacing native species. These introductions are contributing to the imbalance of the marine ecosystem. As well, aquaculture has grown exponentially over the past years in this region and introduced species have raised concerns about their effects on wild Pacific salmon and other native species.

Climate Change
Climate change poses an extensive threat with uncertain outcomes within the ecoregion. Projections suggest that within the next few decades, the region could face less winter snow accumulation, earlier peak spring stream flows, lower summer stream flows, and elevated stream temperatures. This will result in potentially devastating effects to many fish species that migrate up stream, such as salmon.

Increased ocean temperatures and resulting changes in ocean circulation are cause for concern for many other commercial species of fish, such as halibut and rockfish, and marine invertebrates, such as crabs and shrimp. Changes in water current patterns and oceanic processes will affect the distribution of species. This will most likely displace, to some extent, virtually all species, while altering their feeding and breeding habits.