Foyle and Lagan Search and Recue are among 67 charities to benefit from the Department of Transport scheme.
The grants were awarded from a funding pot of £5m being delivered across the UK over a five year period.
Phillip Batt, a founding member of Lagan Search and Rescue, said the money was vital to the group's survival.
The Belfast based organisation is to receive a total of £31,590.
"It's a tremendous boost to organisation, this is our sixth year in operation and we now have three lifeboats and 40 plus volunteers," said Mr Batt.
"We'll be using this vital money mainly for volunteer equipment, such as new life jackets and helmets.
"This highlights the commitment of volunteers, we launch our lifeboat between four and seven minutes and that really is on a par with the RNLI."
The organisation not only deal with local emergencies, they can also be called in to help national search efforts here and further afield.
Some volunteers recently returned from the Aegean Sea where they were involved in rescuing migrants and refugees in trouble at sea.
Their counterparts in Londonderry, Foyle Search and Rescue, have been handed £42,000 - the highest of any of the charities across the UK.
The group have been operating in the Foyle area since 1993 and the bulk of their work involves call-outs for missing or vulnerable persons.
UK Maritime Minister John Hayes said: "Every day countless volunteers in water rescue charities across our island nation carry out vital work during emergencies, not only around our coasts but also keeping our rivers, lakes and inshore waters safe.
"It is imperative that we value and support their tireless efforts. I am delighted to be able to announce the latest round of funding, ensuring they have the equipment and resources they need to provide their round-the-clock lifesaving services," he added.
Two water rescue charities in Northern Ireland have received £70,000 in funding between them.