The poll, which covered 100 retailers, rated the chain “very poor” for value for money and in-store experience.
Homebase/Bunnings and Sports Direct were the next worst performers, while Richer Sounds and John Lewis were at the top of the table.
WH Smith said just 586 customers had commented on its stores in the survey.
“This survey… is neither statistically relevant nor meaningful relative to our loyal customer base,” a spokeswoman said.
“Every week we serve three million customers in our 600 UK High Street stores and have maintained our presence on the high street where many other retailers are closing stores.”
It is the ninth year in a row that WH Smith has been ranked in the bottom two of the survey.
According to Which?, the retailer achieved a satisfaction score of just 50% this time, after consumers criticised its “cramped and messy” stores.
One customer complained that staff were “unhelpful”, while another said their local store was “untidy and too small for comfort”.
It is not the first time the firm’s shops have been criticised – a spoof Twitter account that mocks the state of its carpets has attracted 24,000 followers.
Last week, outgoing boss Steve Clarke admitted it was an issue, telling the BBC it was the “most painful aspect of my job”.
He said for some stores, there was a trade-off between being profitable or redecorating.
Sales at WH Smith’s High Street division have been falling amid challenging trading conditions.
However, group revenue climbed last year as the retailer’s biggest business – concessions at airports and rail stations around the world – expanded by 8%.
Retail analyst Richard Hyman suggested shareholders in the company had pushed it to focus on “short term returns” in its travel division.
“WH Smith understands that in travel locations where you need a different type of shop, it can still represent a good retail option
“But that is much less the case on the High Street where it has been bypassed by many of its rivals.”
According to the Which? survey, DIY chain Homebase/Bunnings was the next worst performer, with customers saying its shops were hard to navigate and that it was “difficult to find staff for guidance”.
Sports Direct also did badly, with one shopper describing the sportswear retailer as having “a very oppressive atmosphere”.
Most of the highest-scoring shops were specialist retailers, with customers commending them for their “expert advice and high-quality products”, said Which?