Investigations into the ongoing issues at South Bay, which was also rated "poor" last year, have revealed bacterial pollution from a number of sources including humans, seabirds and dogs.
Bacteria from industrial effluent may also have an "occasional impact", according to Yorkshire Bathing Water Partnership (YBWP), which commissioned a cutting-edge DNA profiling study,
Scarborough Borough Council is investing £180,000 in new toilet facilities at Vincent Pier, which will include toilet waste disposal for visiting mariners.
YBWP said no single factor was responsible for lowering water quality and they were "fully committed to ensuring that the bathing water quality at Scarborough South Bay improve significantly into the future."
The latest figures from Defra show six beaches in Yorkshire are rated as "excellent," down from 11 last year, which the partnership blamed on the unusually wet summer.
The six "excellent" beaches are Cayton Bay, Danes Dyke, Robin Hoods Bay, Runswick Bay, Tunstall and Whitby.
Those rated "good" are Bridlington North and South, Filey, Flamborough South Landing, Fraisthorpe, Hornsea, Sandsend, Scarbrough North Bay, Skipsea, Wilsthorpe and Withernsea.
Reighton has improved from "sufficient" to "good."
The six others classed as failing in the UK are Clacton (Groyne 41), Essex, Instow, Ifracombe Wildersmouth and Combe Martin in Devon, and Burnham Jetty North and Weston-super-Mare Uphill Slipway in Somerset.
But conditions have improved since 2015, when the new system of classification under tougher EU rules came in.
That year, 12 beaches were classed as failing and the number rated excellent was 264 (63.5%).
Readings taken over the last four bathing seasons are used to determine the annual grade for the bathing spot, with this year's results reflecting how clean the water has been from 2014 to 2017.