Residents in at least 590 homes in Wainfleet and Thorpe Culvert were told to leave as waters continued to surge on Saturday.
The town first flooded on Wednesday after more than two months’ worth of rain fell in two days, causing the River Steeping to burst its banks.
On Friday, three RAF helicopters dropped 270 one-tonne sandbags in an attempt to repair the bank.
Conservative MP for Boston and Skegness, Matt Warman, told the Press Association on Saturday evening that “the Environment Agency is in the process of putting together two pumps that will start taking away some quantities of water”, but he was unsure when they would be up and running.
He also suggested the Environment Agency and other authorities may need to consider in future what could have been done better to prevent the deluge, but said “ultimately, that level of water was always going to cause problems”.
Warman also praised the multi-agency response to the flooding.
He added: “In terms of the response, we have seen an incredible working together of the agencies.
“Local people should keep an eye on the police because there is still the potential for risk to homes and lives.
“But in the long term, it will always just be a huge thank you.”
Lincolnshire police have shared a list of more than 100 postcodes, all in the PE23 and PE24 area, where evacuations are possible.
The force said on Saturday afternoon: “Some occupiers in this area were advised to leave in this area yesterday. Our advice still remains and has been extended to around 300 homes (in addition to the 290 already advised and assisted to evacuate).”
The Maritime and Coastguard Agency are assisting with the evacuations.
They said: “HM Coastguard is assisting other emergency services and authorities in Lincolnshire this afternoon in response to further flooding.
“On Saturday 15 June, HM Coastguard is assisting with the evacuation of approximately 300 properties in Wainfleet.
“Three coastguard rescue teams are on scene through the afternoon and the teams which are responding are from Mablethorpe, Skegness and Wrangle in Lincolnshire.”
City of Lincoln council said the temporary repairs had since “started to deteriorate” and another military helicopter had been deployed to deliver more ballast.
Meteorologist Simon Partridge said: “There is the potential for some thundery and heavy rain on Tuesday and Wednesday. A little bit of uncertainty about when it will arrive but it will be pushing in from the south and will leave from north-east England.
“England and Wales will have spells of heavy and thundery rain.”