Earlier, the rescue helicopter could be seen circling the harbour, particularly around Matiu-Somes Island and a rescue boat was also out on the water.
One person remained in the waves windsurfing but did not appear to be in trouble.
The three-day event features kite surfing, wind surfing and stand-up paddleboarding.
Police earlier said they were unsure how many windsurfers were affected.
"Police would urgently like to hear from any event participants who have exited the water without reporting back to the event organisers," police said earlier.
"We would also like to hear from anyone who has found equipment unattended on the shore."
Based in Eastbourne, Waterbourne includes the New Zealand Slalom Windsurfing Nationals, the Kite Big Air Nationals, SUP racing, the Waterbourne Ocean Clash and the charity Paddle for Hope.
Organisers said earlier in the week that 60 competitors had registered for the competition this year, coming from all over the country and the Pacific.