The wet summer increased pollution on beaches, the MCS said
Last year's wet summer has been blamed for a drop in the number of Scottish bathing beaches being recommended for "excellent water quality".
A total of 41 beaches have made it into the Good Beach Guide, three fewer than last year, and a drop of 15 from the all-time high in 2004.
The Scottish Environment Protection Agency (Sepa) tested 109 beaches around Scotland's coastline.
Storm-related pollution driven by poor weather has been blamed by the MCS.
The Marine Conservation Society (MCS) said its tests, which were held between June and September last year, coincided with one of the wettest summers on record in Scotland.
This caused flood water to mix with sewage gushing from combined sewage overflows, and polluted storm water to run off farmland and city streets into rivers and seas, it added.
Areas including North and South Ayrshire, East Lothian, St Andrews and the Edinburgh city beaches at Portobello were particularly badly affected.
Calum Duncan, Scottish conservation manager for MCS, said it had been warning for years that climate change was likely to increase storm pollution around Scotland's coast.
He said: "If we're to deal with that problem then specific counter pollution measures are required now, including new farming practices, investment in sustainable urban drainage systems, a significant expansion of the sewer system to handle large volumes of storm water and end-of-pipe monitoring on combined sewer overflows."
"We are recommending 41 beaches for excellent water quality this year, which is good, but poor quality bathing water carries health risks.
"MCS advises people to use the Good Beach Guide and do three things; pick bathing beaches with a good water quality record, stay out of the sea for at least 24 hours after heavy storms and report pollution problems to us via the Good Beach Guide website."