The environmental watchdog says the water “may present a risk to human and animal health” and could cause sickness, diarrhoea, stomach cramps or fever.
The warning comes after Ardrossan and Saltcoats Beach in Ayrshire was found to be polluted in a separate incident earlier this week.
NHS Fife, Fife Council and Fife Coast and Countryside Trust are currently working with SEPA to address the issue in the Kinghorn Burn.
Temporary signage has been installed at access points to the beach to reflect SEPA guidance and will remain in place until water quality in the burn has improved.
Anyone who becomes unwell after contact with water from the burn should seek advice via the NHS Inform website at www.nhsinform.scot or call NHS 24 on 111.
A SEPA spokesperson said: “SEPA is continuing to monitor the situation closely, including carrying out further water quality testing. The need for precautionary advice about the water quality in the burn will be kept under review.
“Scheduled sampling of the bathing water will continue as normal and public advice will be updated if any issues at the bathing water are identified.”
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A Scottish Water spokesperson said: “We have been actively carrying out investigations across the sewer network and wider underground drainage networks in Kinghorn to identify and address potential sources of recent high sample results.
“Water quality issues at Kinghorn Harbour Beach have been uniquely complex and challenging, but we are committed to continuing to work with partners to deliver improvements.”
