Two beaches in Lowestoft have kept hold of their Blue Flag status but Southwold Pier has missed out on an award.
Blue Flags are given each year by Keep Britain Tidy in recognition of water quality, safety and cleanliness.
Lowestoft north and south beaches will again be able to fly the blue flag but Southwold Pier, which regained the status last year, will not.
The mayor of Southwold, John Windell, said it was "disappointing" to have missed out.
'Chemicals and sewage
"I think our main concern is what has caused the sea water to be certified in this way," he said.
"We think it's the agricultural run off from the rain water, which can be chemicals and sewage."
Mr Windell said more money should be invested in water treatment works to reduce the amount of sewage going into the sea.
Seventy nine beaches in England were awarded the blue flags - nine more than in 2011.
Suffolk Coastal District Council decided, once again, not to apply for Blue Flag status for Felixstowe beach.
Councillor Doreen Savage said it would have cost up to £15,000 to apply.
She said the water quality and beach had recently been praised by the Marine Conservation Society.
She said: "There are better things to spend money on than flying a flag."