The credit card industry uses batches to settle funds. For example, if you run 10 transactions for $1 each, you will receive one $10 deposit (instead of 10 separate $1 deposits).
In other words, you will not see individual transactions being deposited into your account. You will see groups of transactions, also known as a batch, deposited as a lump sum.
In order to find which batch a transaction has settled in, see How to Find a Transaction's Batch.
The following support article explains how deposits made by PayJunction will appear in your bank account: