The 1990s proved to be a decade of challenge for Bream Bay College.
After many years of staffing stability, a number of experienced staff retired or moved to other schools. Mr Aston had retired at the end of 1989 and was replaced by Jules Flight 1990-1995, and then by John Fitzgerald 1996-2000.

Long serving teachers who left included Deputy Principal Des Olney, Ray McCullum, Clive Craymer, Kevin Fricker, and Kit Singleton, and Brian Vercoe. Between these six teachers were 143 years of service to Bream Bay College.

The completion of the refinery expansion and power station projects saw a dramatic decline in the Bream Bay population. This was mirrored in the drop in the school roll which, having reached a peak of 656 in 1984, the roll dropped to less than 500 for most of the 90s. This had the effect of limiting the number of courses offered at the College, and, together with the loss of experienced teachers, created a negative impression within the community.

However, despite these problems, hard working students and staff continued to take the College forward. Courses were updated and improved, and a new computer room was created. Several successful drama productions were produced by Mrs Raine. Performance Music went from strength to strength. At one stage there were 20 bands within the school. ‘Transient’ went on to win the Northland Rockquest in 1996. Under the tutelage of Ray McCullum, debating teams regularly won the Jack Richards Trophy.

Rugby League gained success with the selection of Brady Small and Anthony Clyde in the New Zealand Under 15 team. The Girls 1st XI Hockey team won the Greenwood Shield in 1992, 1995 and 1994.
The profile of Maori was raised with the introduction of Te Reo Maori as a subject taught to Years 7 – 10. The Kapa Haka group performed successfully Tai Tokerau, and went on a cultural tour to Australia in 1993

The uniform was modernised to white t-shirt/blouse, black trousers, and black or tartan shorts or skirt. The brown jersey was replaced by a terracotta jersey or sweatshirt.