Waimea College diversity captain Cat McNicholl says it would have been an injustice to have left the school with a segregated assembly seating arrangement.

A Nelson school is ditching separating boys and girls at assemblies after a diversity group argued it discriminated against gender diverse students.

The Waimea College decision ends a tradition of 61-years and has been described as a "monumental moment" by a year 13 student who said students should be allowed to decide where they sit.

School diversity captain and school leaver Cat McNicholl said it would have been an injustice to have left the school with a segregated seating arrangement.

Braden Fastier Waimea College pupil Cat McNicholl campaigned to get rid of gender-based seating arrangements at assemblies so they are more inclusive.

"You should feel safe, not discriminated over something as mundane as an assembly," she said.

"Even though it's a tradition, I don't think it is necessary."

Pride members agreed they would prefer to have the option on who they are seated next to, and not be defined by gender.

McNicholl proposed the change, on behalf of the Pride group which advocate for the school's Lesbian Gay Bisexual Transgender (LGBT) community. She discussed it with principal Scott Haines, and deputy principal Graeme Smith.

The college said in a statement it valued student voice and made the change to ensure the school continued to meet the needs of all its students.

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Haines did not want to comment further before parents were fully informed.

McNicholl hoped future Waimea College students would be seated in their respective houses, which were mixed gender.

She intended to stay in touch to see the change through.

There will be other students in similar positions at schools that are affected by this.

The change from segregated seating allowed for more diversity, and individuals to be who they were in the hall, as they could do outside of the hall.

The change had been embraced by students and builds on the culture of the school being a place where people can feel comfortable, and express themselves, she said.

Other co-educational schools in the area Nayland College, Garin College, and Golden Bay High School already follow a mixed seating arrangement.

Motueka High School has surveyed teachers and its student council on the issue.

Motueka deputy principal Stacey Fry said it intended to trial mixed seating arrangements during Term 1 of next year, making it more publicly known that it is accepted for students to sit by who they feel most comfortable with.

Motueka High School also has the same approach with uniform, on including gender diversity, allowing students to wear the uniform they feel most comfortable with.