The heavy rainfall in Picton overnight has caused the sewerage system to back up.
A council spokeswoman said council staff were helping people deal with overflows in houses in York and Buller Sts.
Two pumping stations in Dublin and Surrey Sts had overflowed into Waitohi Stream and into the harbour.
It will take two or three full tidal cycles before the water clears.
Public Health advice is to keep out of the sea at Picton in the meantime and to follow appropriate hygiene practices including thorough handwashing if there is any direct contact with seawater.
Anyone noticing problems with their toilet plumbing should contact the council on 03 520 7400.
- The Marlborough Express