It comes after the quality of water at South Bay dropped from "good" to "sufficient" last year.
A graph on the Environment Agency's bathing water quality website showed a spike in the amount of Intestinal Enterococci - bacteria found in the intestines of animals and humans - earlier this month.
The Agency is looking at all possible sources - including permitted effluent discharges, the harbour and the Gypsey Race - a watercourse which drains a large agricultural area.
In recent years Yorkshire Water has invested £40 million in Bridlington to improve water quality, with work including a new pumping station, sewer and improvements to the existing sewerage system.
As well as weekly spot sampling the Agency plans to do a day of intensive sampling across a full tidal cycle at numerous set points along Bridlington North and South Bays.
North Bay remains classified as "good".
Claire Campbell, of the Environment Agency, said: “We are carrying out a monitoring programme in Bridlington to look at bathing beaches and the things that affect water quality.
“Where bacteria levels are high in a sample we will undertake further analysis to try and identify the source of the bacteria."
Ms Campbell said the public also has a part to play in keeping bathing waters clean, including by not feeding seagulls, cleaning up after dogs and disposing of litter correctly.