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The 19-year-old Napier-based rider had a share of the lead in the competition after the first two rounds of the series, which left two days of high-speed motorcycle racing to go.
Racing on Saturday was near Balclutha, and on Sunday the action shifted to near Mosgiel.
Riders had to ride a course of about 40km in three hours and at the end of that time, the rider who had travelled the longest distance over how many laps of the course was the winner.
About 70 riders took part in the series.
Watts’ main rival was Palmerston North’s Paul Whibley, who was level on points after the two earlier North Island rounds (near Marton and Dannevirke ).
But, with only three rounds to be counted and riders to discard their worst score, it meant nothing was certain until the end of racing on Sunday.
Watts won the race at Balclutha, finishing just 7sec ahead of Whibley in the three-hour senior race, and then repeated the dose at Mosgiel, this time beating Whibley to the chequered flag by 44sec.
Manawatu’s Whibley, a two-time former cross-country champion in the United States, had to settle for overall runner-up, while Raglan’s Brandon Given, Sam "Charlie" Brown of Waikato and Whanganui’s Seth Reardon rounded out the top five seniors.
Taupo’s Wil Yeoman dominated the 90-minute junior grade races on both days at the weekend and the 15-year-old easily wrapped up the junior crown for 2021.
The course in Balclutha was tight and technical while the race on Sunday was a faster, more free-flowing course.
Riders can travel over all different sorts of areas, from open farm paddocks to tight forest hills.