Flash flood warnings remain in place until Monday evening.
Three times the usual rainfall for July fell in a matter of days over parts of the country as 11 regions have declared fatalities, local media reports.
The slow-moving system has already dropped large hail and inches of rainfall in parts of Texas and Missouri.
The Southwest monsoon provides most of northwest Mexico's yearly rainfall.
The floods are just a precursor to the summer monsoon season.
A dozen individuals went missing over the weekend after flooding swept away their vacation home.
Heavy, unseasonable rain over central Texas has left three dead, 12 missing and around 400 homes wrecked.