Palo Alto Puts its Wastewater to Work

Municipal wastewater plants supply an estimated 86% of the inorganic nitrogen entering San Francisco Bay in the dry season, a hefty serving of algae food. The Bay’s huge 2022 bloom brought low oxygen and widespread fish deaths. Now Palo Alto has finished a $4.6 million shoreline pilot to test whether a living landscape can remove more of that pollution before the water reaches the Bay.

The water has already been cleaned at the local treatment plant, but treated water can still carry nitrogen that feeds algae. Getting more of it out matters: regulators now require wastewater plants to cut their combined dry-season inorganic nitrogen discharges 40% from 2022 levels, under limits taking effect in 2034. Palo Alto’s pilot is designed to handle up to 100,000 gallons a day, a small share of the treatment plant’s output with a bigger research job.

Here’s how it works. Underground irrigation sends treated wastewater through an engineered slope of soil and other porous material, supporting native plants above and pollutant-removing microbes below. That planted transition between land and marsh is called a horizontal levee. The design is meant to improve water quality while rebuilding the habitat that a healthy shoreline needs. The useful action is happening under the landscaping, too.

The project grew out of an earlier experiment at Oro Loma in the East Bay. For Palo Alto, restoring marsh-edge habitat was the original goal. The San Francisco Estuary Partnership brought lessons from Oro Loma to Palo Alto, where early design work was completed in 2018. The city and partnership carried it forward with support from the U.S. Environmental Protection Agency, California’s Coastal Conservancy and Department of Water Resources. Construction began in September 2025; the partners celebrated completion this September. Save The Bay volunteers helped grow its plants.

A two-year study at Oro Loma found more than 97% nitrate removal in water flowing through the subsurface. Nitrate is a form of nitrogen; that result gives the approach a promising starting point.

Palo Alto adds an important real-world test. Oro Loma’s experimental system was separated from the Bay; the new pilot is connected to it. That lets researchers investigate what tides, saltwater, sediment and waves do to treatment and habitat over time. Those are practical questions for any city considering a living levee on an actual shoreline. A design that looks good in a controlled experiment still needs to get along with the Bay.

The site also tackles an old ecological break. Local creeks once supplied fresh water to this edge of Harbor Marsh, before development and flood-control channels interrupted the connection. Treated water can help replace that missing supply, supporting freshwater marsh, wet meadow and streamside shrubs. For wildlife, including the endangered salt marsh harvest mouse, those transition areas can provide food, nesting space and refuge from high tides.

The gentle slope creates room for wetland habitat to move uphill as water rises. Plants can also help build up organic soil. Researchers will track how this landscape develops, because the longer-term promise is a shoreline that combines cleaner water with living habitat and sea-level-rise adaptation. Lessons from the pilot are intended to inform larger flood-protection projects in Palo Alto and around the Bay.

That is the bigger deal behind a 500-foot shoreline project. If the treatment and habitat benefits hold up under real conditions, more communities could incorporate this kind of planted edge into future shoreline work, adding another option alongside treatment-plant upgrades. Palo Alto’s construction is complete; its long-term pollution removal, habitat gains and resilience still need to be measured. The pilot’s job is to turn a promising combination into evidence other places can use.

There’s already a relocated, wider trail for walkers and cyclists, with photo stations where visitors can help document the changes. The wastewater has extra work to do. Watching a marsh grow into the job is a decent reason to take a walk.