The Environment Agency, East Riding Council and Yorkshire Water joint probe is set to explore seabirds, bacteria in the sediments in the harbour, seaweed and algal blooms as possible causes.
Environment Agency bathing waters expert Claire Campbell said they hoped the findings would mean action could be taken to improve the quality.
It comes after people were advised against swimming off the beach last year after the Environment Agency sampling deemed the water poor quality.
East Riding councillors heard in December that the cause remained a mystery, especially given waters off the neighbouring Bridlington North Beach were rated good.
Since then, Environment Agency investigations have so far found water quality can be affected by people, seabirds and dogs at different times.
But it has not been able to establish the environmental factors under which they would make bathing water worse.
Sampling at Bridlington South Beach began in July and is set to continue until September to gather more data to help uncover the causes.
They are set to be taken every half an hour from 8am to 6pm on set days throughout the bathing season.
They and other samples taken at Bridlington Harbour and the Bridlington North monitoring point will look first at E. coli and IE bacteria, which are used to determine water quality.
The samples are then set to be sent to an Environment Agency lab where more detailed analysis will be carried out in autumn.
Environment Agency teams will be taking more than 7,000 samples from 424 designated bathing spots across the country, including Bridlington South.
Bathing water expert Ms Campbell said the work in Bridlington would help the Environment Agency to better understand pollution sources.
The official said: “While we will always strive for improvements, overall bathing water quality has improved significantly over the past decade, with a continuing upward trend, due to robust regulation and working with partners.
“In most places, bathing water is now better than it has been for many years.
“We are, however, keen to find out the detail of what is causing our poorer results, so that action can be taken by the relevant people to improve our bathing waters.”
The poor rating for Bridlington South Beach led to events including an annual Boxing Day charity swim being cancelled.
It also sparked concerns from Bridlington South councillors including Tim Norman and Andy Walker about the effect on the area’s tourism industry.
Bridlington South Beach is one of the East Riding’s flagship tourist attractions, with new beach chalets installed there ahead of the summer season this year to meet high demand.
In January, councillors called for urgent action to be taken to improve the quality of bathing water because of concerns over the tourism industry and public health.
But the then council Economy Portfolio Holder Cllr Jane Evison said she feared that overstating the issue could also risk sending tourists packing.
The investigation into the causes of the poor quality rating remains ongoing.