But the estuary’s ecological condition has been classified as “unfavourable” for more than a decade, with vital habitats like saltmarsh, seagrass and shellfish beds in decline.
Rivers to Reef aims to introduce standardised water-quality monitoring to track pollutants and identify hotspots.
The trust will organise bi-annual water quality “blitzes” in collaboration with Earthwatch.
Local clean-ups will be used to stop plastics entering rivers, and check wastewater from homes and businesses is correctly connected to the wastewater drainage system.
The public will be encouraged to help by scraping and binning cooking fats and oils, instead of pouring them down the drain, and correctly dispose of wet wipes.
Rachel Forsyth, chief executive at Aire Rivers Trust, said: “We all rely on our rivers and seas, yet pollution from everyday life is quietly harming them.
“Rivers to Reef is a chance for people across Yorkshire to see the impact they can have, from the stream in their village to the reefs off our coast.
“By working together, we can restore life to our waterways and leave a legacy of clean, thriving waters for generations to come.”