My 16 year old worked under a 1099 for part of the year. Will she need to pay taxes on that?

A minor who makes more than $400 (tax year 2024) in self-employment income will typically have to pay Social Security or Medicare taxes, regardless of their total earnings.

At What Income Does a Minor Have to File an Income Tax Return?

This is income from self-employment.  If your daughter is required to file a tax return, this income must be included on Schedule C.  If the amount of net profit from self-employment is over $433, filing a tax return is required because self-employment tax must be paid.