Wash Mussels Ltd will create five "limited" test areas on the bed of the River Stour where 500 tonnes of mussels would be laid each year.
The RSPB is concerned about the impact of dredgers and farming on rare birds.
A public consultation runs until October.
In 2014, the company applied for a licence for a five-year trial, but objections were raised about a lack of studies on the effects on wildlife.
The RSPB is worried about an adverse effect on the tens of thousands of birds, particularly goldeneye and red breasted merganser, which use the estuary, which has European Special Protection Area status.
Mark Nowers, RSPB conservation officer, said: "Any development needs to show these important species are not affected."
Peter Scott, solicitor for Wash Mussels, said: "There will be limited operations and no equipment in situ, because there will be no ropes or nets.
"Noise from dredgers is pretty insignificant in terms of bird disturbance.
"If the trial is successful, there will be significant employment in dredging and preparing the product for market."
Mr Scott said it would not put buoys on the river or sink pots to catch crabs which feed on mussels.
The Essex and Suffolk Wildlife Trusts said they would be reviewing the company's data as part of the public consultation which runs until 7 October.
The Department for Environment, Food and Rural Affairs (Defra) said it would consider the results of the consultation before deciding whether a licence should be granted.

The 24-year-old victim was subjected to a serious sexual assault by two men in Dixon Road, in the city's Govanhill area, in the early hours of 19 May.
Police Scotland launched a high-profile inquiry after the incident.
The force said two men, aged 28 and 29, had been reported to prosecutors following the inquiry.
Large scale mussel farming could deter rare birds feeding on a "tranquil" river estuary with protected status, wildlife groups have warned.
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Two men have been reported to the procurator fiscal over the alleged rape of a woman in the south side of Glasgow earlier this year.