Club president Greg Stewart said stormwater from parts of the adjoining Wavy Knowes subdivision flowed both directly and indirectly on to the course, and he blames the council for letting it happen.
However, the council said the flows were natural and it was not required to act.
The course had always been afffected by surface flooding, but drainage and pumps could cope with the water.
That was until about five years ago, when the flooding worsened and took longer to dissipate.
The water took, on average, two and a-half weeks to drain, which wiped out play for the club's more than 300 members.
Before learning stormwater from the subdivision, established in 1996, was flowing on to the course, the club had spent $15,000 on two new pumps and hired contractors to remove silt and debris from the internal water courses, Mr Stewart said.
When club members approached the DCC, council staff inspected the site and suggested a pumping station would need to be installed to transfer the water to the adjoining Kaikorai Estuary, at a cost of $250,000, he said.
But the council "kept changing its mind about whose problem it was" and the club was pushed from department to department trying to get help.
Mr Stewart believed stormwater should not be allowed to be discharged on to another ratepayer's land, and the council should not have signed off on the subdivision when such discharge would occur.
"There are rules for everyone and they seem to be breaking them."
In October, the club approached the Saddle Hill Community Board and asked its help in dealing with the council.
Council water and waste services network manager Rezaul Haque said council staff would prepare a report and present to the board at its next meeting in February.
It would contain options to alleviate the flooding, but responsibility for any action would sit with the club.
Before the development of the subdivision, stormwater from the site naturally discharged through a channel on the golf course to the estuary.
Because the stormwater from the subdivision was following the same, natural, course, "council has no power to stop this", Mr Haque said.
"We do not have any law to stop rainwater going to other properties."
However, he added that a new subdivision code of practice, introduced in July this year, included measures that would require the effect on downstream properties to be investigated as part of the consent process.
The subdivision increased stormwater run-off by about 15%, which was not "significant", he said.
Another issue that would have contributed to the flooding was increased rainfall in the past five to 10 years.
The duration of rainfall had shortened, but it had become more intense, Mr Haque said.
"We have issues throughout all of Dunedin."
Mr Stewart remained adamant the council should take responsibility for allowing the stormwater to flow on to the club's land.
The council was "trying to weasel out of it", he said.
The club's committee had raised the option of legal action before and was prepared to take it if "that's what it comes to".
