According to Us Weekly, the couple grew apart due to their hectic schedule.
Cooper, 40, started dating 23-year-old Waterhouse in 2013. They had never been shy to show their affection to each other, but they rarely discussed their relationship in interviews.
"I don't talk about my boyfriend because it's boring," Waterhouse once told Elle UK.
Cooper was once married to actress Jennifer Esposito who tied the knot with British model Louis Dowler last year. His other ex Zoe Saldana whom he dated on and off before seeing Waterhouse is also now happily married. She has twin sons with husband Marco Perego.