Very high levels of bacteria caused by human and animal feces are finding their way into island waters, according to a shoreline survey conducted by the city and the Kitsap County Health District.

About 20 percent of the 133 areas surveyed exceeded the health district’s threshold for fecal coliform; E.coli is also present in the troubled areas, according to results.

Testers also have identified three failing septic systems – two at Crystal Springs and one at Fletcher Bay – that are leaking directly into the water. Samples in those areas were “exceedingly high,” according to officials.

Owners of those systems have been notified and are making necessary repairs, said Health District Program Manager Stuart Whitford.

In the meantime, the county is discouraging the harvesting of shellfish near Crystal Springs and Fletcher Bay; those who do harvest should thoroughly cook their catch.

Though not good news, the findings aren’t surprising, Whitford said.

“We had had complaints (at Crystal Springs), including last year when we had a report from a septic system designer,” Whitford said. “We selected the area for survey because it had been on the city’s radar since the late 1990s.”

The city paid the county $20,000 for its help with the survey, which began last month and will continue through June. The city hopes to eventually do more detailed testing after they’re done with the current work, though funding for that may require state grant money.

Two of four rounds of samples have been taken so far at various pipes, streams, bulkhead drains and stormwater conveyances around the island.

Test areas include the south shore of Eagle Harbor, and along the island’s southwestern shoreline, from Lynwood Center to Fletcher Bay.

Those areas were chosen based of pollution found there more than a decade ago, when the state Department of Health did a survey of commercial shellfish programs in the area.

This time around, parts of Crystal Springs showed acceptable levels of bacteria, while others were cause for concern. The area from Point White to where Baker Hill Road meets Crystal Springs Drive is particularly problematic because the drainfield there is so close to the water. Poor soils and a high groundwater level – due to the springs for which the area is named – also contribute to the problem.

Once specific areas of concern – dubbed “hot spots” – are identified through samples testers then investigate to find a source, which can include wildlife, septic systems, pets or livestock.

When a failed septic system is the suspected culprit, testers flush colored dye down a toilet connected to the system. If the dye emerges on the beach, residents know it needs to be fixed.

Finding a definitive source of pollution can sometimes be difficult, Whitford said.

“The second phase is going to be the tough part because the sources aren’t so easy to identify as a failed septic,” he said. “It’s very tedious work.”

Weather can impact readings, as happened recently with samples taken at the south shore of Eagle Harbor.

“They were good samples, but they were done on a day that was pretty dry,” Whitford said. “In some areas, the bacteria rises when it rains. With more pipes flowing during a rain event, you’ll find more samples.” He said that three more surveys will be taken at Eagle Harbor’s south shore.

Future survey areas may include Rockaway Beach, which has similar issues to Crystal Springs.

Like Whitford, City Water Resources Specialist Jalyn Cummings said results so far have mostly matched expectations, though she was slightly surprised by the number of hot spots testers found.

“It should certainly create a sense of awareness,” Cummings said. “But this is not a cause for panic. We’re doing the survey to find these hot spots – in the past decade it’s just been a question mark.”