The accident prompted a warning from the lake enforcement and education officer, Shayne Hitchcock, for boat users to avoid that section of the lake while the water was high and discoloured.
A Queenstown-based helicopter landed on an exposed sandbank next to the grounded boat to transport the woman to Dunedin Hospital.
The 41-year-old woman, whose name has not been released, was treated and discharged from hospital last night.
Sergeant Ian Kerrisk, of Alexandra, said two adults were in the boat, towing their two primary school-aged children on inflatables behind the boat.
The woman was standing up watching the children, facing the back of the boat.
''When the boat has hit the sandbank and run aground, she's been thrown backwards and sustained head injuries.
''We're satisfied alcohol was not a factor and there's no suggestion that it's anything other than a significant crash with unfortunate results,'' Sgt Kerrisk said.
The accident happened near Panners Cove.
The Clyde Coastguard was initially called but was stood down because owners of private boats at Cromwell, who were closer, offered their assistance.
Constable Paddy Henderson, of Cromwell, who was on duty, was one of them.
The boats ferried St John ambulance staff to the grounded boat and later transported the woman and her family to the exposed sandbar and then to the shore.
The family was taken to the Cromwell Medical Centre to be checked over and then travelled to Dunedin to be with the injured woman, Sgt Kerrisk said.
Mr Hitchcock said there had been several groundings of boats in that area this summer and when the water was discoloured, as it was now, it was impossible to tell where the clear channels were through the sandbars.
A red marker buoy near the site where the accident happened had been placed to indicate shallow water.
''Because both the two rivers [Clutha and Kawarau] are high, the silt and sedimentation shift all the time, so the channels change. But there are signs at all the jetties warning about the hazard. It's been getting worse and even if you're familiar with that part of the lake, you can still get caught out and run aground.''
He had been on the lake this week recommending that boat users avoid the Kawarau arm while the water was high and discoloured.
''My warning would be not to go there, or if you have to, travel with extreme caution.''
The hazard posed by the sediment had been around for many years and there was no way of marking the clear channels, because they changed all the time, depending on the lake flow and the level of sediment.
''It's still navigable water, but just like when you're driving a vehicle - it comes down to skipper responsibility, I guess.''
Although groundings in that area were frequent, the only other injury accident he could recall happened last year, in a similar place to yesterday's one.
In that case, a person received minor injuries, Mr Hitchcock said.
