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This is not the best weekend to spend some leisure time on one of New York City’s waterways.

The city’s Department of Health and Mental Hygiene has advised residents to avoid direct contact with the Hudson River, East River, New York Harbor, Jamaica Bay and Kill Van Kull until continued water quality testing by the Department of Environmental Protection deems it safe for recreational use. The waters were contaminated when untreated wastewater flowed directly into them from treatment plants overwhelmed with flooding or power outages in Hurricane Sandy’s wake.

The state Department of Environmental Conservation has received reports of 12 facilities that experienced flooding, ten that reported partially treated or untreated wastewater flows since Monday and four that are still discharging sewage, according to Gov. Andrew Cuomo’s office. A press release stated “there is no accurate way to determine the amount of partially treated or untreated flows entering waterways.”

This issue of raw sewage getting into otherwise-safe water is partly a result of the fact that New York City has outdated infrastructure. These days, it is standard for municipalities to separate their systems for collecting wastewater and storm water — bringing the former to a treatment plant and the latter directly back to rivers and lakes. But cities like New York have combined systems that take in both sewage and rain water and bring all of it to treatment plants. This becomes a problem in times of heavy rains or extreme weather like hurricanes, when the systems can overflow and release untreated wastewater.

This poses obvious health and environmental concerns. One Environmental Protection Agency report for the New York region lists the various pollutants that could be released in the event of sewage overflows — including bacteria like E. coli, viruses, and industrial waste like oils and metals. Though actually drinking the contaminated water is the most likely way to get sick, people can also fall ill after eating fish from the water, swimming in it or inhaling its vapors, according to the report. Diarrhea and nausea are the most common symptoms.

Floodwater in general is not safe for these reasons, which is why Mayor Michael Bloomberg has advised to throw away food that has come into contact with it and disinfect belongings. Both Bloomberg and the Department of Environmental Protection have said that the city’s drinking water supply is still safe.

Even before Sandy hit, the state Department of Conservation and city Department of Environmental Protection were looking into ways to start building new infrastructure to help prevent sewage overflows. In March, the agencies signed onto an agreement under which the DEP is tasked with evaluating solutions for combined sewage systems along ten water bodies: Alley Creek, Coney Island, Hutchinson River, Flushing Creek, Gowanus Canal, Bronx River, Jamaica Bay, Westchester Creek, Flushing Bay and Newton Creek. Work is beginning now for Alley Creek and the DEP is expected to submit its findings for each area to the DEC over the next five years.

Modifications to the sewer systems are an option, as well as additions to the system, like retention tanks to hold any overflows or barrels that could catch additional storm water before it meets with sewage. The DEP has estimated that it has spent $1.8 billion on the past to deal with discharges from the sewer systems and is expected to spend an additional $1.6 billion on upgrades, along with $730 million on green initiatives, like rain gardens.

According to the DEP, approximately 1.2 billion gallons of wastewater are treated at one of the cities 14 plants on an average day. There are more than 400 points around the boroughs where discharge from the combined sewer systems is permitted.