The shellfish farmer seeking to grow oysters and scallops in the Niantic River on Thursday filed a new application, which amends his original 2016 proposal, with the Waterford-East Lyme Shellfish Commission.

Tim Londregan’s new application requests access to two areas in the river, which the commission would lease to his company, Niantic Bay Shellfish Farm, as part of the commission’s evolving process for allowing the use of the river for commercial shellfishing.

Londregan's application is the first test of a newly developed application process and comes at the same time that the commission is considering revisions to its aquaculture plan, which had not been updated since 2002.

The commission was forced to reconsider its approach to allowing commercial shellfishing in the river after it developed an agreement with Londregan that was met with opposition from property owners and business people on both sides of the river last summer.

Londregan said Thursday that his application includes plans to install shellfishing nets and gear in two spots on the river: one just north of the Niantic River bridge, and another off the Waterford shore near Niantic River Road and 10th Avenue.

Both areas were already outlined in the commission’s 2002 plan allowing for commercial fish shellfishing in the Niantic River. Londregan said only 0.9 acre between the two areas would be taken up by shellfishing gear at any given time.

The commission accepted his new application Thursday and will send copies to both the East Lyme and Waterford harbor commissions, which each have jurisdiction over one of the areas proposed in Londregan‘s application, for their comment.

The requirement that the commission send commercial shellfishing applications to the harbor commissions and subsequently hold a public hearing on the proposal are part of the new application process the commission developed, with the help of Waterford’s town attorney, after residents of both towns objected to the commission’s handling of Londregan's 2016 application, the first commercial shellfishing venture the commission had ever considered.

Londregan, who operates a shellfishing operation in the Niantic Bay that supplies oysters and scallops to local and regional restaurants, said Thursday that his new plan to use the river would be smaller than his original proposal, a concession to those neighbors and local business owners concerned that a commercial shellfishing operation would impede boating and affect tourism in Waterford's Mago Point neighborhood.

He said he could amend his proposal if any part of it doesn't align with the final version of the commission's shellfish plan.

"I'm pretty flexible," he said. "Over the last 28 months I've made several concessions."

Londregan, with the support of the state Department of Energy and Environmental Protection, argues that introducing growing scallops and oysters into the river will improve its water quality and benefit the population of shellfish available for recreational collection, which has fluctuated in recent years.

His original agreement with the Waterford-East Lyme Shellfish Commission granted him access to a 5-acre area in the middle of the river, in which he planned to leave juvenile scallops and/or oysters to grow before moving them into the Niantic Bay to further grow to market size.

The commission rescinded that agreement late last year and has been forced in the face of public outcry to consider revisions to its shellfish plan and develop the new application process.

The commission members, along with Waterford Town Attorney Robert Avena and Planning Director Abby Piersall are drafting updates to the shellfish plan that they plan to release before a public hearing this spring.

The new plan keeps in place the five areas in the river outlined in the 2002 plan available for lease by commercial shellfishing operations, but clarifies the process for leasing one of those areas and enforces a two-year experimental period during which any applicant must prove that their project is viable and doesn’t harm the river or species living in it.

Waterford-East Lyme Shellfish Commission Chairman Peter Harris said Thursday that he hopes to schedule a public hearing at which people can comment both on the proposed revisions to the shellfish plan and Londregan's application in the same day.

m.shanahan@theday.com