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Tap & Dough bistro owner Norma Emerson said "a shower of raw sewage'" was emerging from the corner of Mold St and Snow Ave in the Strath Taieri town.
Her business had been sandbagged but if the rain restarted as predicted she believed the premises would be inundated with wastewater.
"It's just a matter of time.''
A fire crew and council staff were on the scene, she said.
In a media release this morning, the Dunedin City Council said three streets in Middlemarch were closed due to "surcharging from the wastewater network".
"Overall the stormwater and wastewater networks are running well,'' the release said
Council network contracts manager William Clifford said it was dealing with surface stormwater flooding and wastewater surcharges in the town.
"Three roads are closed and an extra pump is being used to support the wastewater system.
"We're focusing on protecting houses and businesses but some flooding is likely.
The amount of flooding would depend on rain levels over the rest of the day and any flooding would take a while to lower after the rain eased off.