Forging sanctuary partnerships was taken to an unprecedented new level in 1994 with the creation of Water Quality Protection Programs (WQPP) in Florida Keys and Monterey Bay National Marine Sanctuaries. Recognizing that water quality is key to ensuring protection for all sanctuary resources, Monterey Bay National Marine Sanctuary worked with other federal, state, and local partners to take an ecosystem-based approach, integrating the expertise of regional resource agencies to protect water quality in the sanctuary and its watersheds. Six specific, collaborative plans have been developed to address the issues with the highest potential to affect sanctuary water quality.

Good water quality is also critical to the health of coral reefs, mangroves, and seagrass habitats of Florida Keys National Marine Sanctuary. To better understand how humans have an impact on water quality and how those changes affect sanctuary habitats, the Water Quality Protection Program was created in 1994 through a partnership that includes NOAA, the EPA, and the State of Florida. In 2002, state waters of the sanctuary were declared a No-Discharge Zone for vessels and in 2010 the federal waters of the sanctuary followed suit.