Nathan started Rowing for St Thomas of Canterbury in 2006.

In 2016 Nathan Flannery competed in the men's quad at the Final Qualification regatta in Lucerne in May with the hope of qualifying for the Rio Olympic Games. The crew finished third, one place outside of qualification but late removal of the already-qualified Russian men's quad allowed entry for the New Zealanders. Despite the late call up and interrupted training the crew finished fourth in the B Final.

Nathan first represented New Zealand in 2010 at the Junior World Rowing Championships in the men's quad, in 2011 he moved into the under-23 team where he raced in the men's quad. In 2012 Flannery teamed up with Hayden Cohen in the double scull at the U23 World Rowing Championships and took away the gold.

In 2013 he moved into the elite team in the men's quad where they won silver at the first World Cup of 2013 in Sydney.

Rio 2016 will be Nathan's first Olympic Games. Nathan started Rowing for St Thomas of Canterbury in 2006.

He went on to represent New Zealand at the World Rowing Junior Championships where they got Bronze in the men's quadruple sculls.

In 2012 Nathan paired up with Hayden Cohen to become Under 23 World Champions in the men's double sculls.

Nathan was also in the elite men’s quadruple sculls in 2013 and 2014.