Govaerts, representing the Zenith club, won two junior titles for the Makos.
He claimed the 100m breaststroke title in 1min 8.40sec and the 200m breaststroke title in 2min 30.05sec.
The Makos also dominated the senior men's breaststroke as Hokitika swimmer George Schroder won over 100m and 200m.
The other leading swimmer from the South Island team was Tasman junior Sam Mckenzie, who won the boys 200m and 400m freestyle.
A handful of other Otago swimmers joined Govaerts on the podium.
Andrew Trembath (Neptune) showed his class with victory in the men's 100m backstroke in 58.16sec.
Kate Godfrey (Neptune) won the women's 200m backstroke and was second in both the 400m and 200m individual medleys, and Carina Doyle (Neptune) had two thirds, in the women's 200m and 400m freestyle.
In the junior ranks, Caitlin Deans (Neptune) had two seconds, in the 400m and 800m freestyle, and Nicholas Pryde (Neptune) was second in the 1500m freestyle and third in the 400m freestyle.
The Makos finished second overall on 1750.5 points, behind the Harlequins - Northland, Auckland and Counties-Manukau - on 1978.
The zonal championships featured 160 of New Zealand's leading and promising swimmers against each other in an American-styled collegiate competition.
Regions in New Zealand were divided into four zones to compete in relay formats in two non-stop two-hour sessions. Each zone team comprised 40 swimmers split into junior and senior teams.
Olympic swimmer Steven Kent helped lead the way for the Harlequins and his winning swim in the 200m freestyle counted for some valuable extra points, as each zone nominated a joker who could earn double points for their swim.
The night concluded with swimmers taking part in a 1000m freestyle relay for all swimmers in the senior and junior divisions.
In the junior relay, the Makos managed to hold off the Harlequins, who worked their way up from last to second with the help of an impressive leg from Gabrielle Fa'amausili. In the senior relay, the Harlequins managed to storm home ahead of the Makos.
