GCA chief executive Gillie Westwood said a fall in sales in the pest and aquatics category for instance, which is largely made up of wild bird food sales, could be attributed to "customers cutting out luxury purchases".
She added: "We can't blame the weather and I would have hoped for better."
But she said: "If you compare garden centres to the high street we're still faring well."
British Retail Consortium figures for UK retail sales values for September were 0.3 per cent higher on a like-for-like basis from September 2010, when sales had risen 0.5 per cent. On a total basis, sales were up 2.5 per cent, against a 2.2 per cent increase in September 2010.
Total BRC non-food sales are up 0.1 per cent in the last three months.
GCA figures show year to date sales are up 0.75 per cent overall on 2010.
September had 108 per cent of the average sunshine for the month in the UK and 79 per cent of the rainfall in England and Wales, although in Scotland rain was 129 per cent of the average.
See Horticulture Week 21 October for more.