The deputy, who is a Vice-President of the European Parliament, made the call in a letter which has been sent to Phil Hogan, the European Commissioner for agriculture and rural development.
With the focus currently on the floods in Texas, McGuinnes said, "The north western regions of Northern Ireland and Ireland have been badly impacted by extensive flash flooding."
McGuinness, who is a member of Parliament's agriculture committee, added, "In the Donegal region, many families are displaced and there is serious structural damage to buildings, bridges and rural roads. In Northern Ireland, the situation is very similar with extensive damage to homes, properties and roads."
The EPP group MEP went on, "The damage to agricultural holdings in the region is substantial, including significant loss of winter feed and extensive damage to potato and grain crops. There was also a severe loss of poultry flocks in the floods."
Her appeal comes with the US city of Houston currently under a night-time curfew as it battles the impact of hurricane Harvey.
The storm has dumped record rainfall, leaving large parts of the Texas city underwater, homes destroyed and more than 20 people reported dead. Thousands of people have fled their homes in search of emergency shelter amid severe flooding.
Responding to the Texan floods, the European Commission said it was providing emergency aid to the US authorities.
EU foreign affairs chief Federica Mogherini said, "The EU knows very well how devastating natural disasters can be and our thoughts and solidarity are with all the American people affected by this deadly hurricane. The US can count on the EU as a strong and an historic ally for all our support."
Further reaction to the devastating floods came from European Commissioner for humanitarian aid and crisis management Christos Stylianides, who said, "Our EU emergency centre is giving a helping hand to our American friends as they work tirelessly to deal with the devastation of hurricane Harvey."
He added, "The EU's emergency mapping service has been put into action and we stand ready to help further in any way we can."
On Wednesday, a Commission spokesperson said, "Our 24/7 emergency response centre has been in regular contact with the US Federal Emergency Management Agency (FEMA) over hurricane Harvey and any EU support that could help the US authorities.
The EU's emergency service has been activated at the request of FEMA and it is now providing damage assessment maps."
Meanwhile, Gianni Pittella, leader of Parliament's S&D group, has called for the EU to deliver help to Sierra Leone "with the utmost urgency" after floods and landslides in the country's capital Freetown took a huge toll on human lives.
The Italian MEP said, "This is an ongoing tragedy that could get even worse if we don't help the survivors. Many have been left with no shelter and with nowhere to go. The EU must react with the utmost urgency."