Krishna Kumar timed 29 minutes and 24 seconds to finish ahead of his team-mate Pranav Kumar (29:25). Ramjith, also of MEG, claimed the bronze in a time of 29:42.
Navya Shenoy led a Basavanagudi Aquatic Centre sweep in the girls under-18 category.
Navya won the gold in 33:11 and was followed by Shifa Akram and Ashwini L.
Results: Boys under-18: Krishna Kumar (MEG, 29:24) 1; Pranav Kumar (MEG, 29:25) 2; Ramjith (MEG, 29:42) 3.
Under-15: Sanu Saju (MEG, 17:12) 1; D Mayur (BAC, 17:18) 2; Pramod Yadav (MEG, 17:32), 3.
Girls under-18: Navya Shenoy (BAC, 33:11) 1; Shifa Akram (BAC, 34:39) 2; Ashwini L (BAC 35:20), 3.
Under-15: Chandana (PM Swim Centre, 17:52) 1; Anvitha Shampur (BAC 19:02), 2; Ashitha (PM Swim Centre, 19:32), 3.