ShapeShift uses a flat miner fee of 0.003 BTC for every Bitcoin transaction we facilitate regardless of the size of the transaction. This relatively high miner fee ensures that our users are able to receive their funds as quickly as possible without experiencing delays due to network congestion.
In the event that your Bitcoin deposit is returned to you because it did not meet the requirements to be accepted by our system, you will notice that it is 0.003 BTC less than your original deposit amount. This is the miner fee required for us to send your Bitcoin back to you in a timely manner.
This can disproportionately impact smaller value transactions. For example, if you attempt to deposit 0.007 BTC to ShapeShift for an exchange but the timer has expired and the funds are returned to you, you will be refunded 0.007-0.0021=0.0049 BTC. While this might seem drastic, ShapeShift does not profit off of this miner fee in any way and it is necessary to minimize delays experienced by our users.