Loch Fyne on the west coast and the Bay of Firth, Orkney - known as world-class destinations for seafood like oysters, scallops and mussels - are among the worst affected beauty spots.
It follows data from publicly-owned Scottish Water in April which showed sewage was dumped into rivers, lochs and seas 24,398 times last year.
Run-off from Scotland's 31,000-mile sewer network is only supposed to spill into the environment during exceptionally bad rain.
The dumping scandal in England has seen private firms like Thames Water hit with multi-million pound fines over breaches but no action has been taken here.
The Lib Dems, who analysed data on discharges into shellfish waters, warned the findings put the world-renowned reputation of Scotland's £14million shellfish sector at risk.
Scots party leader Alex Cole-Hamilton hit out, saying: "We knew of the impact sewage was having on our rivers and beaches, but now we learn sewage is also being dumped in protected shellfish waters.
"Shellfish production is an important industry for Scotland and our coastal and island communities. They deserve better than having sewage dumped in waters linked to their livelihoods.
"It's time the Scottish Government started taking the sewage crisis more seriously, rather than handwaving all concerns by pointing to the situation in England."
Lib Dem analysis of Scottish Water sewage figures found 3785 discharges between 2023 and 2024 into shellfish water protected areas, as designated by environment watchdog Sepa.
Sewage was dumped into these waters for 22,936 hours.
Orkney's Bay of Firth saw the most frequent discharges with sewage being dumped 1446 times across the two years.
And iconic Loch Fyne saw the longest duration of sewage being discharged, for a total of 6260 hours across 2023 and 2024..
With the next Holyrood election looming in just seven months, Cole-Hamilton highlighted Scottish Liberal Democrat plans for a new Clean Water Act.
This would "bring our sewage network into the 21st century, clamp down on dumping and get to the bottom of this disgusting practice", he added.
Last year, more than 2.5million oysters and 11,690 tons of common mussels were produced from Scottish waters.
A SEPA spokeswoman said: "The quality of coastal waters can be affected by a number of factors, including from rural diffuse pollution, wastewater discharges and combined sewer overflows.
"We have required Scottish Water to produce the Improving Urban Waters Routemap which sets out a delivery plan to improve discharges from Combined Sewer Overflows and improve understanding of when and where discharges occur.
"Scottish Water has since installed 1000 new monitors at sewerage outfalls within 2km of all designated shellfish and bathing waters. This near real-time information is now available to the public on Scottish Water's overflow map.
"We will continue to monitor Scottish Water's progress against delivery of the Routemap commitments, using our regulatory powers if required."
The Scottish Government said: "We designate Shellfish Water Protected Areas (SWPAs) to protect water quality and support the sustainable development of the shellfish industry.
"Once an SWPA is designated SEPA works with Scottish Water and others to ensure the appropriate levels of protection are in place to continue to safeguard water quality."