Thurstaston beach has been branded a health hazard after failing minimum water quality requirements for the second year running.
It means beach-goers face unacceptable levels of bacteria in the sea according to a national study.
Three of the borough’s shorelines were given the highest rating of "recommended" by the Marine Conservation Society’s Good Beach Guide.
The rating means beaches at New Brighton, Moreton and Meols have once again met European standards for excellent water quality and that “local sewage discharges are treated appropriately.”
Councillor Brian Kenny, Wirral’s cabinet member for the environment, said: "The MCS acknowledges the North West was one of the wettest areas in the UK last summer.
"Thurstaston beach is subject to heavy rain and surface water run-off from surrounding farmland which affects the quality of bathing waters.
"Although the council is not directly responsible for managing water quality, where we can we will continue to work with other agencies to improve the water quality at all our beaches."
He added: "Overall, it is really encouraging to see that like last year, Wirral still boasts three out of five ‘recommended’ North West beaches in this year’s Good Beach Guide."
Tests showed Thurstaston did not improve on last year’s result and West Kirby slipped down a rank from "guideline" to "basic pass" - just the minimum requirement for water quality.
Across the UK, 461 beaches were given the top "recommended" award for having excellent bathing water quality in the guide, the third highest number in the guide's 24-year history, and a significant increase on last year.
Some 42 more bathing spots reached the top grade in 2011 than in 2010.
But 46 failed to meet even the basic standards of water quality set in European law 35 years ago, a slight increase on last year's figure of 41.
Rachel Wyatt, MCS coastal pollution officer said: “From 2015 Europe’s beaches will be classified using even stricter water quality standards due to the revision of the Bathing Water Directive.
"But instead of viewing these new standards with dread, our coastal communities and water companies should welcome them as an opportunity to attract more people to the UKs wonderful and varied seaside resorts.
“The next few years are critical as the quality of the UKs bathing waters can play a vital role in the economic recovery of our traditional seaside resorts.
"Making sure their local beaches are ready to comply with the revised Bathing Water Directive is a huge opportunity for local authorities and chambers of commerce to attract increasing numbers of tourists to the UK’s coastline.”
Monitoring for the new standards begins next year, and if a beach consistently fails to meet these legal limits between then and 2015, signs could be set up advising people not to enter the water.
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