The Football Association, the Premier League and Sport England have made available the funds, which will be administered by six County FAs in the north of England.
FA chief executive Martin Glenn said: "Once the scale of the impact of the recent storms became clear, the FA and its funding partners came together to make funds available."
Sport England had already announced it would initially invest up to £200,000 to help sports facilities affected.
League Two club Carlisle were also affected, with Brunton Park flooded, and Saturday's game against Notts County will be at Preston's Deepdale ground.
The situation was so severe at Brunton Park that Koi Carp fish were found swimming in the goalmouth.
But as a Football League team Carlisle will not benefit from the fund.
Grassroots football clubs affected by flooding caused by Storm Desmond will be provided with a £750,000 emergency fund by the sport's supporting bodies.