The GLWQA was amended again by protocol in 1987. New concepts of ecosystem-based management were incorporated including the development and adoption of ecosystem objectives for the lakes.

The Protocol also included two new annexes focusing on provisions to develop and implement Remedial Action Plans (RAP) to restore impaired water uses for significantly degrades areas around the Great Lakes (known as Areas of Concern, like the Detroit River) and Lakewide Management Plans (LaMP) to address whole lake contamination by persistent toxic substances.

Several other new annexes were also introduced, further broadening the scope of the Agreement: non-point contaminant sources; contaminated sediment; airborne toxic substances; contaminated groundwater; and associated research and development.