Heather Watson was born on Guernsey to Michelle and Ian Watson. Her mother is from Papua New Guinea and her father is British, the managing director of Guernsey Electricity from 1995 until retirement in 2010. She has one brother and two sisters. Heather Watson started playing tennis at the age of seven, and at age twelve she went to the Nick Bollettieri Tennis Academy in Florida.
In 2006, Watson won the British Under-14 Championship. The following year she won the British Under-16 Championship, and reached the semifinals of the British Under-18 Championship. She lost in the Under-18 semifinals again in 2008 to eventual winner Tara Moore. In October, Watson travelled to Pune in India to compete at the 2008 Commonwealth Youth Games. There she won the gold medal, winning the final against Kyra Shroff. Mother Michelle left her job in 2008 to travel full-time with her daughter around the World Junior Circuit.