Fingal County Council has advised the public not to swim at 12 beaches because of worries over the water quality, while Wicklow County Council has issued an advisory notice about the quality of bathing water in Bray.
A spokeswoman for Fingal Co Co said heavy rain over the weekend led to an overflow at the pump stations.
That means rainwater that would normally flow through the sewers and into the waste water treatment works instead flowed out to sea.
The council is awaiting test results on the water quality, but has issued the advisory as a precaution. The results should be known in 48 hours.
Red flags have been placed on the beaches, with blue flags taken down from Balcarrick beach in Donabate, Portrane beach, Skerries South beach and the Velvet Strand in Portmarnock.
The advisory notice applies to Balbriggan beach, Loughshinny beach, Skerries north beach, Skerries south beach, Balcarrick Beach, The Brook beach, Tower Bay beach, Malahide beach, Velvet Strand beach, The Burrow beach, Claremont beach and Hampton Cove.
The council says it expects the closure will be temporary.
Meanwhile, Wicklow County Council has said tests are being carried out at Bray North and South promenades.
A council spokesman said it is suspected that heavy rainfall may have led to sewage being discharged from the waste water treatment plant or the sewer network.
The test results are expected by the end of the week, so the notice will remain in place until then.
Elsewhere, a prohibition notice that was in place at Brittas Bay North, because of high levels of intestinal enterococci, has been lifted.