Staithes was the only beach in Yorkshire and the Humber to fail to meet the mandatory values when measured in 2008 in a list of UK beaches and inland swimming spots.
The Government vowed last week to boost efforts to clean up the coastline after the latest European report criticised the quality of water at more than two dozen resorts.
Sandsend and Runswick Bay beaches, which fell short of the mark in 2007, have improved so significantly they now go beyond meeting the mandatory standards and meet the guide value set by the European Commission.
The majority of coastal areas in the region are up to standard.
The latest report is based on 2008 water cleanliness tests carried out at more than 21,000 bathing spots around the 27 EU countries.
Staithes bathing water also failed to get into the Good Beach Guide this year for the 17th time in the past 21 years.
Scarborough Borough Council's head of environmental services Andy Skelton said last month: "Problems with water quality are understood to be linked to naturally occurring discharge from surrounding land which runs downstream and into the harbour.
"The Environmental Agency and the council are continuing to look into the issue to see if anything sensible and cost-effective can be done."
"We're working to improve sewerage systems and are aware of the effect heavy rain and flooding can have on our coastal bathing waters," said a government spokesman.
"The proposal to make connections to sewers subject to meeting national standards will result in less water reaching sewerage treatment works and consequently reduce the risk of flooding and pollution."
The Department for Environment, Food and Rural Affairs said it is currently tackling pollution from agriculture source, including grants to build fences between livestock and watercourses and advice to farmers on reducing water pollution.
The commissioner for the environment, Stavros Dimas, said: "High quality bathing water is essential for the well-being of European citizens and the environment – and this goes for all other bodies of water too.
"I am pleased to see the overall quality of water in bathing areas is improving throughout the union."