Tim Sanson lives on 24ha near Lake Ellesmere and the eels use the creek on his property to breed and migrate.
A breach in a nearby seawall meant that when it flooded, the creek was engulfed and they were carried onto the land, he said.
"As soon as the eels get a sniff of the salt water, they're off across the paddocks, trying to get to the sea. Unfortunately, the last high tide last night wasn't high enough for them to get across and they've been stuck there."
There are thousands of eels, writhing in masses on the now dried ground.
"No creature deserves to go out that way and the seagulls are having a field day. The sun's taking its toll on them and unless we do something really quickly, they'll perish."
It was an awful sight, Mr Sanson said.
"I'm going to try and scoop them out and get them off to sea as best I can.
"Last night, as high tide was approaching, I would have, just as a rough guess, thrown about 500 over into the sea."
But for every one he picked up, there would be many others he could not get to, he said.
Sanson believed this was all preventable. He said he warned the Canterbury Regional Council and Selwyn District Council that this would happen more than a year ago, contacting them multiple times to fix the sea wall to no avail.
"When we got the big flood last year, probably about 30 to 40 of that was covered in water and silt.
"This year, the whole farm's been covered. It almost got in the house... it's buggered now, covered in salt water. It's no good for anything."
He holds local authorities responsible for not acting after locals hosted them last year to show them the problems.
With no hills between his property and the nearby communities of Lincoln and Leeston, Sanson was worried the flooding would spread even further if the councils did not act soon.
"The whole point of it is to build that wall, keep the sea back as long as we can to give everyone an opportunity to plan for the future."
Water has gone over roads in the area, damaging them and adding a strain on ratepayer's coffers, he said.
He was worried what he would find when the water fully drained off his property.
A natural phenomenon - Ecan
Both councils confirmed they have staff there to try and move the eels to sea.
The Canterbury Regional Council confirmed several thousand eels have been returned after becoming stranded.
But its field operations general manager, Leigh Griffiths, said thousands of shortfin eels - which are a taonga species - also died.
"It's important to note this is a natural phenomenon where tuna are migrating to sea at this time of the year. In the absence of a lake opening, the tuna will follow any pathway where a flow of sea water is present.
"Depending on the tidal flow and beach profile, they unfortunately can find themselves stranded and perish. This is an annual, natural phenomenon which is all part of the heke tuna [eel migration]."
Griffiths said it was aware of a number of coastal properties impacted by erosion, swell and flooding, and the council was working to identify hazard zones along the Canterbury coast.
"Coastal erosion is a concern for many coastal landowners and the issue is exacerbated by climate change," Griffiths said.
"The regional council doesn't collect rates to manage coastal erosion on private land or fund repairs - it's something private landowners need to address.
"We do, however, have a dedicated staff member who works with the community to clarify and help them understand what they can do to protect their properties, such as through private stopbanks and the moving of debris."
Selwyn District Council infrastructure and property group manager Murray Washington said the council maintained the land drainage network in the area.
"But it does not have the mandate to carry out land remediation works on the beach or on Mr Sanson's private property," he said.
"The council has worked with Mr Sanson around all areas where we have an ability to assist and staff and volunteers have been onsite today assisting with the clear up of the eels."
