The U.S. Environmental Protection Agency said Monday it has approved removing another official “impairment” for the St. Louis River Estuary and Twin Ports harbor.

The agency said the “excessive loading of sediments and nutrients’’ impairment has been successfully dealt with, at least as far as being a legacy issue. It’s the third of nine impairments that have been dealt with in the estuary, while six more remain.

Researchers concede that the St. Louis River and its neighbors like the Nemadji River still pump tons of sediment into Lake Superior every year, but they say the problem isn’t being caused by legacy issues from the past.

The Areas of Concern program was developed to deal only with legacy issues caused by the first century of development and pollution. But it wasn’t designed to deal with continuing or modern problems like new chemicals of concern, agricultural waste, urban runoff and stream banks that continue eroding today.

For the lower St. Louis River, legacy issues included unregulated discharge of industrial and municipal waste, dredging and filling in the estuary, and wood waste deposited in the river from extensive logging upstream — all of which caused erosion and sedimentation problems. Many of the nutrient issues improved when municipal and industrial sewage was treated effectively. Recent projects have made headway removing wood waste left by sawmills a century or more ago.

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“Results from multiple studies showed a dramatic decline in nutrient concentrations and sediment loading in the Area of Concern,’’ the EPA said in a statement Monday. “While certain tributaries showed higher sediment levels, this was due to the natural condition of loose clay soils in those valleys. Studies of the sediment-rich bays showed that the turbid waters were not inhibiting healthy plant and animal communities.”

A team of technical experts, agency partners, staff and stakeholders agreed that "multiple lines of evidence demonstrated that the removal targets outlined in a plan to resolve the impairments." The effort was led by state and tribal agencies and funded by the federal Great Lakes Restoration Initiative.

In addition to the sedimentation and nutrient impairment being removed, impairments for aesthetic degradation (2014) and fish tumors (2017) also have been removed. Historic legacy impairments still being worked on include fish contamination that makes some fish unsafe to eat; reduction in fish and wildlife populations; degradation and destruction of fish and wildlife habitat; restrictions on where dredging material can be placed due to contaminants; degradation of small aquatic life; and beach closings due to high bacteria levels.