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Innovation in Malindi: Treating Waste with Sanivation to Save Reefs in MPAs
By Rosanna Hine | June 13, 2025
Along Kenya’s northern coast, the waters off Malindi and Watamu’s Marine Protected Areas (MPAs) are home to vibrant coral reefs, seagrass beds, and mangroves — ecosystems that support more than 600 species of fish and over 250 types of coral. These reefs also anchor the country’s ocean economy: marine tourism alone contributes over 90% of the sector’s GDP share. But as coastal towns grow, so do their wastewater problems.
“There’s a long history of looking at overfishing and climate change as the main threats,” says Peter Musembi, an ecologist with WCS Kenya. “But pollution? Aside from a handful of studies, it has largely flown under the radar.”
In 2022, WCS began investigating just how much untreated sewage was flowing into the reefs around Malindi and Watamu. What they found confirmed the stakes: a combination of open dumpsites, flood-prone latrines, and illegal sewage disposal could be introducing high levels of bacteria and nutrients into the water. The risk? Coral disease, algae blooms, and reduced reef resilience.
“Sanivation is developing a waste-to-value treatment plant in Malindi that not only treats waste but turns it into clean-burning briquettes for industrial use — reducing both ocean pollution and deforestation.”
To respond, WCS partnered with Sanivation, a social enterprise transforming human fecal waste into biomass briquettes. Sanivation is developing a waste-to-value treatment plant in Malindi that not only treats waste but turns it into clean-burning briquettes for industrial use — reducing both ocean pollution and deforestation.
This circular model has real potential: Sanivation aims to process 60% of Malindi’s waste and divert 200,000 tons of it from coastal ecosystems by 2027. With interest from the Global Funds for Coral Reefs (GFCR) to support this cause, WCS began the monitoring component — testing for ecological and water quality indicators like Enterococci and caffeine to track whether the reefs are bouncing back.
“We’ve never had a project quite like this,” Peter says. “It’s not just about toilets. It’s about reef health, climate resilience, and creating new income streams.”
The model is now being scaled. With funding lined-up from GFCR, WCS and Sanivation are working to see the Malindi and Watamu projects replicated in other coral reef refugia such as in Kwale County which is home to part of the proposed Kenya–Tanzania Transboundary Conservation Area (TBCA). A concessional loan from GFCR is under development to support this expansion, alongside technical collaboration with local governments, water utilities, the Kenya Wildlife Service and Pwani University.
“This is our first time linking sanitation directly to reef health,” says Naomi Korir, Research Lead at Sanivation. “It’s a learning curve, but the potential for impact is huge.”
For Naomi Korir, Research Lead at Sanivation, the lessons go beyond engineering. “This is our first time linking sanitation directly to reef health,” she says. “It’s a learning curve, but the potential for impact is huge.”
As the project moves forward, WCS continues to play a catalytic role — applying its Coastal Pollution Toolkit, advising on policy, and helping build the long-term monitoring systems needed to track success and replicate it elsewhere.
“Everyone knows what happens when the fish disappear,” Peter says. “Now we’re helping communities understand what’s upstream of that, and how to fix it.”
Rosanna Hine is an Water Pollution Intern with the WCS Global Marine Program.
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WCS is leading efforts to elevate wastewater pollution as a critical ocean and climate issue — bridging science, policy, and partnerships to drive collaborative change for our oceans and for the health of coastal communities. This story is part of a three-part series launched during the 2025 UN Ocean Conference, showcasing the work that WCS and partners are doing all over the world to tackle land-based pollution.
