The Environment Agency warning was issued late on Sunday ahead of more heavy rain falling.
A second alaert for the River Tove from Towcester to Cosgrove, including Silverstone Brook was added on Monday morning.
Amber flood alerts are the lowest of three levels on the government's warning system and experts believe properties are unlikely to be in danger, although an update is expected early on Monday.
A spokesman said: "Over the last 24 hours we have seen heavy rainfall in the River Nene area. This means that the River Nene is now rising, which will lead to flooding of low lying land and roads close to the river.
"We expect the river to remain high throughout the next 24 hours. Our forecasts indicate that flooding to properties isn't likely and therefore flood warnings are not expected to be issued.
"We are constantly monitoring river levels, and have staff in the field checking for blockages and clearing weedscreens. Please avoid using low lying footpaths near local watercourses and plan driving routes to avoid low lying roads near rivers, which may be flooded. "
A Met Office yellow warning for wind accompanied by heavy rain is in force across the county until around 1pm on Monday.