The story of stormwater runoff in Washington is a tale of two cities. In one, rain mixes with sewage; in the other, it’s separated. But neither is sending pristine water into the Potomac and the Anacostia.

Two-thirds of the city is categorized as MS4 (municipal separated storm sewer system) and one-third CSS (combined sewer system), said Meredith Upchurch, who works for the Infrastructure Project Management Administration of the city’s Transportation Department. She leads the team that is about to begin construction of RiverSmart Green Alleys projects in two Northwest neighborhoods.

The problem with CSS is well known: During downpours, it sends untreated human waste into Rock Creek and the two rivers. But MS4 water carries “a lot of heavy metal pollutants — copper, zinc, lead,” Upchurch said. “You get phosphorous and nitrogen that come off the planted areas, or from fertilizers. You get E. coli, bacteria from pet waste or other animal waste.”

The Green Alleys project will retrofit an area just west of Georgia Avenue in Petworth (a CSS zone) and one centered on Quesada Street in Chevy Chase (served by MS4 pipes). Three kinds of permeable surfaces will be installed — concrete, asphalt and preconstructed pavers — and rainwater-retention areas will be added.

The goal is to “either keep the water out of the storm sewer system and the streams altogether, or clean it up,” Upchurch said. “Let it filter through the soil, through the plants, through the mulch, so it captures those pollutants before the water goes into those streams.”

Meredith Upchurch of the D.C. Transportation Department, near water-retention plants and permeable pavers on Third Street SE. (Mark Jenkins/For the Washington Post)

The two updates, budgeted at $3.5 million, are demonstration projects, funded by an Environmental Protection Agency grant through the National Fish and Wildlife Foundation, said Steve Saari, an environmental protection specialist for the city’s Environment Department. Construction is set to begin this month and conclude in December.

The Transportation Department has already constructed some Green Alleys in Northeast, in a neighborhood near Nannie Helen Burroughs Avenue. But the results of that 2012 effort have not been systematically measured.

The Petworth and Chevy Chase areas were selected “partially because the alleys were in poor condition and needed to be updated,” Saari said. But the locations were also chosen because the effect of the changes can be easily quantified.

“You can trace the sewer pipes. They go to a single point where it transitions into the rest of the sewer system,” Upchurch said. “There has been monitoring equipment there to measure the current volume of runoff. Then after we construct the RiverSmart Washington project, we’ll monitor again at the same point and determine the change in volume.”

Runoff should already be somewhat diminished because of the RiverSmart Homes program. The citywide project, administered by the Environment Department, funds stormwater retrofits for 1,000 D.C. homeowners a year. Up to $1,200 per household is available to pay for rain barrels, tree planting, rain gardens, removal of impervious surfaces and replacing grass with native plants with deeper roots.

For the Petworth and Chevy Chase project, “we really wanted to get more homeowners on board, and we also wanted to do more work,” Saari said. “So we offered up to $5,000 on each individual home.”

Of 136 property owners, he reported, 64 participated. That’s a little less than half, with the split almost 50-50 between Petworth and Chevy Chase.

The Green Alley neighborhoods aren’t the only areas where the city has encouraged water-retention projects. There are privately funded rain gardens in the Yards development along the Anacostia River near Nationals Park.

Not all soil will effectively filter rainwater. In urban areas, the ground can be compacted into near solidity by building and transportation uses. And some dirt is just naturally dense.

“Ideally, you would want to build one of these systems and have the water flow through and into the ground,” Upchurch noted. “When the soil is really sandy or loamy, the water can flow through. But we have a lot of clay soils in the District.”

In such cases, a Green Alley includes a layer of gravel and an underdrain that feeds into sewer lines. “We don’t want the water to stand there for more than 72 hours,” Upchurch said.

Because most people don’t like mosquitoes in their back yard anymore than they do heavy metals in their water.