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The 16-year-old King's High School pupil was the pick of the 12 Otago swimmers at the meet, who returned to Dunedin with nine gold, three silver and five bronze medals.
Govaerts won the boys 16-18 years 200m freestyle, individual medley and breaststroke, and the 50m and 100m breaststroke.
The 200m freestyle was particularly close, as he pipped Ryan Curtis, of Auckland Grammar School, by just 0.20sec to win the final in 1min 59.83sec.
His win in the 100m breaststroke was also a close thing, as he had to hold off Jack Weston, of Rotorua Lakes High School.
Govaerts touched the wall in 1min 8.80sec, which was slower than his time in his heat (1min 8.22sec), while Weston was 0.36sec back.
The King's High School pupil also finished fourth in the 50m and 100m freestyle.
Columba College pupil Gabrielle Trotter (14) won two golds in the girls 14 years section, and was involved in a couple of thrilling finishes with fellow Otago swimmer Cecilia Crooks, of St Hilda's Collegiate.
Trotter came from behind to pass Crooks, who went out strong and led for the majority of the race, with 8m left.
Trotter finished in 2min 13.46sec, while Crooks clocked 2min 14.43sec for her silver medal.
The finish between the pair was even closer in the 400m freestyle, as they went stroke for stroke the majority of the race.
However, Trotter, who turns 15 this week, beat Crooks at the touch to claim her second gold medal in 4min 41.48sec. Crooks, who also won bronze in the 200m individual medley, recorded a personal-best 4min 41.61sec for silver.
Trotter was also a part of Columba's under-15 200m freestyle relay team, which won gold. The team of Trotter, Meg Sycamore, Devon Familton and Caitlin Deans clocked 1min 55.98sec to beat St Cuthbert's College by half a second in the final.
Deans won the other gold medal over the three-day competition in the girls 15 years 400m freestyle, when she edged Rudy Adsett, of Napier Girls' High School, by 0.20sec.
Deans touched the wall in 4min 29.16sec, and also went on to win bronze in the 200m individual medley.
In addition to helping Columba win gold in the 200m freestyle relay, Familton snared silver in the girls 15 years 200m freestyle and bronze in the 50m, 100m and 200m backstroke.
The South Island championships will be held at Moana Pool from September 26-28.