Sylvia Johnson said the alarms began at 4am every day, typically sounding every half hour after that.
She said, "The environmental health (department of Eastbourne Borough Council] came down and said they did not really think it was a problem but if you are being woken up at 4am every day I can assure you it is.
"It is making us miserable, when people have to get up for work the next day."
She said residents of the Piazza apartments could not open their windows at night because of the siren and added, "We are all complaining and getting nowhere fast."
The sirens have been put on the lock gates to alert people to when the barriers are coming down.
The latest barriers were installed in May on the advice of the Health and Safety Executive, and the new sirens are louder than those that preceded them.
Premier Marinas marina manager Janet Taylor said the old sirens had often been ignored, adding, "We had to use the new sirens because people are still walking onto the locks as we go to open them and getting trapped.
"Then we have to reverse the whole process and if people do become trapped it is very dangerous."
But she said the volume of the sirens had been turned down since they were installed and the speakers repositioned to face inwards into the locks to limit the distance the sound travelled.
The klaxons are followed by a recorded voice reminding people to clear the lock as the barrier is about to lower.
A spokesman for Eastbourne Borough Council said, "Environmental health officers have gone down and looked at the sirens and listened to them going.
"They are continually working with the residents and the harbour office to find a solution that is a compromise between public safety and a satisfactory level of noise for the residents in the area."