After a card batch closes, your processor moves the net proceeds to your bank account via ACH (Automated Clearing House) the next business day. Most processors absorb the ACH cost, but some — particularly aggregators offering 'instant payout' upgrades and a few legacy ISOs — charge a per-deposit fee. The fee is small individually ($0.10–$1.00 per batch) but adds up at $20–$30/month for a daily-batched merchant.
Distinct from the 'instant payout' or 'next-hour funding' fees that processors charge to expedite the transfer (typically 1.0%–1.5% of the batch). Standard next-business-day ACH funding should be free or near-free — if you see a meaningful per-deposit fee on your statement and you don't use instant payouts, it's worth disputing.