Nurseries increasingly focus on plants that can be mass produced so the big stores can sell them cheaply, he says.
"You have these vast wholesale nurseries now supplying supermarkets - and that's a diminution of choice," he told Radio 4's You and Yours.
However, the Horticultural Trades Association (HTA) says supermarket sales actually help grow the market.
According to Kantar World Panel, nearly 40% of gardeners get their plants, bulbs and seeds from supermarkets.
"That's bad," says Don. "It's rather like the vast suppliers supplying food - you get lots and lots of the same thing mass produced to be as cheap as possible."
The UK garden market is worth around Â£5bn, with some Â£1.4bn spent on garden plants by UK consumers in 2013, according to the HTA, the industry body.
The Gardeners' World presenter believes consumers should shop around.
"I'm a huge fan of independent nurseries. That is where you get the expertise, it's where you will find people who have devoted their life to growing something.
"They will grow geraniums or trees and they will really know about it, so when you contact them, they can give you great help and assistance."
Martin Simmons, HTA director of operations, said: "People often make impulse purchases of plants in supermarkets and if this then encourages them to buy more plants then this is good for the industry and helps to grow the market.
"Buying a plant in a supermarket may be the first step for some consumers, particularly younger ones. If this grabs their interest they will naturally seek out garden centres and retail nurseries."
Waitrose told the BBC it took quality seriously, and that its plants were supplied by two reputable nurseries who supply only garden centres - not other supermarkets.
Inviting Monty Don for a visit to talk to buyers, Asda said it works with a network of expert growers to ensure it offered quality.
Sainsbury's said it had a longstanding relationship with suppliers, many of whom were family businesses. It added that it always worked to give customers choice and value.
The BBC first broadcast Gardeners' World in the 1960s, making it one of the longest running shows on TV. Monty Don presented it from 2003 to 2008 and returned to the helm in 2011.
Supermarket plant sales are reducing customers' choice, says Gardeners' World presenter Monty Don.