Glassford (22) won in 16min 43.35sec from Jeremy Tasker (Oamaru), 16min 47.52sec, and Jake O'Grady (Ashburton), 17min 05.13sec.
The Otago and Canterbury championships are both being held at Moana Pool this week because the Christchurch earthquakes wrecked the QE2 pool.
Andrew Trembath (Neptune) was third in the Otago championships in 17min 19.75sec and O'Grady took the Canterbury title.
It was a solid performance by Glassford, who was still tired after a busy two weeks at a training camp with his coach, Gennadiy Labara.
Glassford impressed with his ability to sustain his technique even though he was under pressure from Tasker and the gruelling 30-lap course.
Glassford always held a slight margin over Tasker (18), who was fourth in the event at the New Zealand short-course championships at Wellington in September.
With two laps to go, Glassford held a body length over Tasker. He then increased the margin to three body lengths at the finish.
Tasker trained with Shane Jones when he was a pupil at Waitaki Boys' High School, and was still feeling the effects of a training camp that the Oamaru club held at Wanaka over the last two weeks.
His time was 15sec slower than his best.
''I got into a groove and was not able to lift my pace,'' Tasker said.
''I knew he [Glassford] would push the pace at the end.''
Tasker will study marketing and commerce at the University of Otago this year and intends to join one of the Dunedin squads.
Trembath (16) lowered his 1500m time by 56sec despite feeling the pain after just 500m.
''My muscles ached,'' he said.
''I am not used to racing this distance. It was hard work.''
Thomas Heaton (Waves) was a convincing winner of the boys aged 14 and under title in 17min 04.73sec. He was followed home by three Canterbury swimmers who took the medals at the Canterbury championships.
The Canterbury champion was Satori Dobbie (QE2), who won in 17min 45.76sec from North Canterbury swimmers Angus Syme, 17min 54sec, and Bryn Atkin, 17min 54.43sec.
It was a huge long-course personal best time for Dobbie by 1min 13sec and a best of 35sec when converted from his short-course time.
Angus Macauley (Oamaru), a pupil at St Kevin's College, finished fifth in the race but was second in the Otago championships. His time was 18min 33.51sec.
He is coached by Shane Jones and his best events are the 200m and 400m freestyle that will be held later in the championships.
The senior women's 800m was won easily by Sarah Cutler (Waves) in 9min 25.52sec, from Stef Gillespie (Zenith), 9min 33.24sec, and Jessica Schneiders (Neptune), 9min 35.68sec.
Cutler has continued her steady improvement and is now the best female distance swimmer in Otago.
Brittany Tucker (QE2) was fifth in the race in 9min 51.46sec and was the Canterbury champion.
Lucy Clough (Ashburton) won the girls aged 14 and under 800m in 9min 43.56sec and was the Canterbury champion.
She was followed home by Caitlin Deans (Waves) in 9min 51.63sec and Zara McLellan (Timaru), 10min 05.94sec.
Deans (13), a pupil at Columba College, is the Otago champion. She won a bronze medal in the 400m freestyle at the New Zealand junior championships last year.