The chopper took Harper, Premier Greg Selinger and other local MPs over flooded farmland and washed out roads.
"Obviously we are here to express our solidarity with people as I know everybody is very concerned about the situation," Harper said after he attended a briefing with emergency personnel at Brandon City Hall. "Many have been affected."
The river is lapping up against farm buildings and raised roads but hasn't forced any evacuations so far in Brandon.
The floodwater coming from Saskatchewan prompted Manitoba Premier Greg Selinger to declare a state of emergency Friday and ask for military assistance to prepare communities west of Winnipeg for the crest.
Selinger thanked Harper for deploying the military so quickly. There are 500 soldiers on the ground right now helping in the flood fight, he said.
But he said there are some "very stressed communities" in southwestern Manitoba where "50 per cent of the land was covered by water."
"As that water abates, we're going to be in there working closely with them to put the infrastructure back in place and get people moving again," Selinger said "That's our objective is to put everybody back to normal as quickly as possible."
Brandon was pummelled Saturday by a violent, windy storm which dumped rain onto the soggy dikes and uprooted trees.
The first crest from a torrent of floodwater coming from Saskatchewan appears to have hit Brandon, provincial flood official Steve Topping told a news conference Sunday.
The crest is below the devastating 2011 flood level, although levels further downstream are still forecast to be higher than 2011.
Officials say the dikes are holding but people living by the swollen Assiniboine River should be prepared to leave at a moment's notice.
People aren't expected to be evacuated unless there is a breach in the city's dikes.
"The storm did not impact the dike," the city said in its flood update Sunday morning. "Any water on the streets was rain water, not river water."
Harper said he's been talking with Selinger and Saskatchewan Premier Brad Wall about the situation but didn't commit to any financial assistance over and above what Ottawa already provides.
"I want to assure everybody that all levels of government are working together very hard," he said. "There will be disaster assistance in this case as there always is according to the federal law. We'll keep on top of this until we get the crest and get through it all."
Some 300 soldiers from CFB Shilo near Brandon responded Saturday, filling hundreds of thousands of sandbags to help fend off the rising floodwater. Major Mike Legace, with the Canadian Armed Forces, said the troops are trying to fill 125,000 sandbags a day as the crest bears down on southwestern Manitoba.
The soldiers are trying to protect 350 rural homes — 150 of which could be flooded if the province deliberately breaches a dike to take pressure off the Assiniboine River.
Cutting through one of the dikes at Hoop and Holler Bend in southern Manitoba could ease some of the pressure on dikes holding back the swollen Assiniboine, but Selinger said it will only be done as a last resort.
Selinger ordered that done in 2011, deliberately flooding the same swath of land and threatening homes in the area in order to save hundreds more downstream.
On Sunday, Manitoba's deputy minister of infrastructure and transportation, Doug McNeil, said pavement on top of the dike has been removed just in case the cut needs to be made.
Work continued Sunday to shore up dikes further downstream to make sure they would hold.
This summer flood was caused by torrential rain last weekend is expected to topple records set in 2011, which was one of Manitoba's worst floods.
A second crest later this month is anticipated on the Assiniboine River at Brandon, but Topping said it will be much lower than the current crest.