According to the local council, neither Dobbies nor any other garden centre have submitted an application for the site.
A Stapeley representative said: "At present, there are complications with the development plans. We are in consultation with the local planning authorities."
She added: "The garden centre is to cease trading at the end of the year due to a downturn in sales during the past two years, which has sadly led to redundancies.
"We will, however, be open every day this year except Christmas Day with many reductions and one-off clearance prices."
The Angling & Outdoor Centre will remain open next year and trade as usual, with a view to possibly being relocated locally in the near future.
Stapeley was granted outline planning permission some time ago to relocate the water gardens within the existing site area and to build offices and up to 150 houses.
An East Cheshire Council representative said no other planning application had been received for the site.