The initial deposit counts toward the annual contribution limit. HSAs and traditional or Roth IRAs have no extra allowance for "seed money." [IRS HSA rules](https://www.irs.gov/publications/p969), [IRS IRA rules](https://www.irs.gov/retirement-plans/plan-participant-employee/retirement-topics-ira-contribution-limits).

Using your hypothetical $3,250 HSA limit, you could deposit the full $3,250 when opening the account if you were eligible for that amount and had made no contributions for the tax year. That would use up your allowance for the year. Employer contributions count toward the same limit. Money routed through an ordinary savings account also counts as a contribution when it enters the HSA. [IRS Publication 969](https://www.irs.gov/publications/p969).

Moving existing funds between tax-advantaged accounts follows different rules:

- You can transfer an existing HSA balance or make an eligible rollover from an HSA or Archer MSA without using your annual contribution allowance. A qualifying IRA-to-HSA transfer does count toward that allowance. [IRS HSA transfer rules](https://www.irs.gov/publications/p969).
- Eligible rollovers into an IRA, such as from a 401(k), and transfers from another IRA generally do not count toward the annual contribution limit. A newly opened IRA could therefore start with a substantial balance from existing retirement funds. [IRS IRA rules](https://www.irs.gov/retirement-plans/plan-participant-employee/retirement-topics-ira-contribution-limits).

There is no cap on the total account balance under these annual contribution limits. Your balance can grow beyond them through contributions over multiple years and investment earnings. [IRS HSA rules](https://www.irs.gov/publications/p969), [IRS IRA guidance](https://www.irs.gov/publications/p590a).