The airport said its £16bn plan for expansion included addressing flooding from Thames tributaries that burst their banks early in 2014.
The Environment Agency, which has plans to meet Heathrow bosses in the next week, said it was "very encouraged".
"I believe this scheme will happen," said spokesman David Murphy.
In February last year, flooding affected homes and businesses along the river in Berkshire, Surrey and the London boroughs of Kingston and Richmond.
The River Thames defence scheme involves reducing the flood risk between Datchet and Teddington by building a flood channel and improving three weirs.
The government announced in its autumn statement it would contribute £220m towards the scheme, with businesses and utility companies being asked to chip in.
Leader of Surrey County Council David Hodge has said Heathrow would be one of those asked to contribute.
Heathrow said its expansion plan included a "once-in-a-generation" opportunity to address issues like flooding from nearby rivers, particularly the Colne and Wraysbury.
"We will work and support the Environment Agency and local authorities in developing better flood alleviation schemes to protect homes and property located away from the airport."
The Airports Commission is currently considering three options for expanding airport provision in south-east England.
It is due to make its final recommendation to the government in the summer.
Mr Murphy, Environment Agency executive for the River Thames scheme, said: "One of the key factors of expansion at Heathrow will be to manage water associated with that development.
"This whole area has many rivers many lakes and therefore water management is incredibly important because of the potential for flooding which we saw last year."
Heathrow airport could be among businesses contributing to a £300m River Thames defence scheme if it gets the go-ahead to expand.