Baker was in a class of her own in the women's contest, clearing out to win in 1:03.27 to be in the top 10 on overall times.
It was the third straight national 5km title for the 21-year-old Baker, who lives on the Gold Coast.
She finished nearly three minutes clear of Taranaki's Charlotte Webby who out-sprinted Australian Emily Seymour for second.
Baker and Radford completed an excellent weekend after earning places in the final Olympic open water qualifier in Portugal in June with their performances in the 10km race on Saturday.
Results:
5km men overall: Kane Radford (Rotorua, HPC) 59:30, 1; Josh Richardson (Australia) 59:34, 2; Michael Mincham (Waterhole, Auckland) 1:00.31, 3; Casey Glover (Capital, Wellington) 1:00.33, 4; Jonathon Pullon (Waterhole) 1:00.36, 5.
Women: Cara Baker (Howick Pakuranga, Counties Manukau) 1:03.27, 1; Charlotte Webby (Aquabladz, Taranaki) 1:06.01, 2; Emily Seymour (Australia) 1:06.11, 3; Shelby Wilson (Fairfield, Waikato) 1:12.17, 4; Grace Sommerville (Ashburton) 1:08.56, 5.