BRISTOL, R.I. — Pollution from a variety of sources in both Rhode Island and Massachusetts continues to contaminate Mount Hope Bay and the Kickemuit River, and often forces areas to be closed to shellfishing and swimming.

Last year, both bodies of water were placed on the Clean Water Act’s annual list of impaired waterways because of one or more water quality issues.

The state Department of Environmental Management (DEM) recently completed a federally mandated water quality restoration study that addresses long-standing bacteria-related impairments to Mount Hope Bay and the Kickemuit River estuary.

Mount Hope Bay, which forms the northeast corner of the Narragansett Bay estuary, and its tributaries, including the Kickemuit, Lee, Coles, Quequechan and Taunton rivers, exhibit elevated levels of fecal coliform bacteria, particularly after heavy rains. Elevated levels of fecal coliform bacteria impair recreational uses in the bay and cause the frequent closure of shellfishing beds following a half-inch or more of rain.

Pollution from stormwater runoff, combined sewer overflows (CSO), failing and improperly maintained septic systems and leaking sewer lines forces the closure of approved shellfishing areas within Mount Hope Bay and the Kickemuit River estuary to shellfish harvesting on an average of 180 days per year as a result of bacterial contamination, according to DEM officials.

In 2006, the DEM took 500 samples from Mount Hope Bay during both dry and wet weather. The difference in water quality is distinctly noticeable.

“After heavy rain events, sanitary quality in the area markedly and quickly deteriorates,” said Brian Zalewsky, of the DEM’s Office of Water Resources. “A majority of the pollution comes from Fall River down the Taunton River. But we do have some sources in Rhode Island that need to be addressed.”

Among those local sources in the Mount Hope Bay watershed contributing to the problem are failed septic systems and substandard cesspools, most notably in North Tiverton, and leaking sewer lines in Bristol and Warren, according to the DEM.

Sampling conducted during wet weather by DEM’s Office of Water Resources and the Massachusetts Division of Marine Fisheries also found that stormwater outfall pipes at various locations around the bay contribute to localized degradation of water quality.

A 24-inch culvert on Robert Gray Avenue, for example, is a big source of pollution during wet and dry weather.

Both the DEM and the Massachusetts Department of Environmental Protection are preparing reports to address the Mount Hope Bay watershed’s contamination problems.

Although more than 70 percent of Mount Hope Bay is in Rhode Island, more than 90 percent of its drainage basin is in Massachusetts. CSOs from Fall River, Mass., are the largest source of fecal bacteria into Mount Hope Bay during heavy rains, according to the recent draft study. However, ongoing construction of facilities in Fall River to store and treat its CSO has begun to mitigate this source of contamination.

The city of Fall River features a sewer system with about 180 miles of sewer line and 11 pump stations. Heavy rains cause frequent CSOs at 19 locations throughout the city that discharge into Mount Hope Bay, the Taunton River and the Quequechan River.

It has been estimated that historically, at least until the operation of the Fall River storage tunnel, about 1.5 billion gallons of stormwater and untreated and/or partially treated sewage were discharged annually into Mount Hope Bay. This was the largest source of fecal coliform bacteria into the bay during wet weather, according to previous studies.

Additionally, during the past decade, a number of municipalities within the Taunton River watershed have implemented measures to address sewage discharges. Taunton, for example, made upgrades to its wastewater treatment plant in both 2001 and ’02. As a result, the number of CSO events there has dropped.

Despite the ongoing efforts of the 10 Massachusetts communities and five Rhode Island communities located partially or primarily within the Mount Hope Bay watershed, pollution remains a problem.

More than 100 types of pathogenic microorganisms can be present in water that is polluted by fecal matter (typically animal waste) and/or phage (its presence is more indicative of human waste than animal) and can cause outbreaks of waterborne disease, according to the DEM’s 2009 draft report.

In order to meet federal water quality standards during both dry and wet weather, significant reductions in identified sources of contamination must be accomplished, according to the DEM. The states’ two studies will establish requirements for those pollution sources.

These recommendations will complement existing pollution reduction efforts in the Mount Hope Bay watershed, such as the Fall River CSO abatement project and stormwater management programs being implemented by cities and towns throughout the region, according to the report.