Depending on the type of cryptocurrency that is deposited, the crypto network itself will charge a fee for the transaction, and any cryptocurrency that is deposited is moved internally for further processing. For example, if you were to deposit 0.005 Bitcoin, the final deposit amount might be 0.0049 after 0.0001 was to paid to the bitcoin miners for the internal transaction. (This is just an example and is subject to change for Bitcoin or any other network — transaction fees will change depending on network activity.). In this example, 0.0049 BTC would be the credited deposit value.
The network fee is not a fixed percentage of the amount, as the blockchain transaction cost is not based on the transaction amount. So it is typically advantageous to deposit larger amounts or make one deposit with the full intended amount rather than several smaller deposits. Furthermore, by using a blockchain with low transaction costs (like Stellar) for deposits, this kind of fee can be avoided.