When Windows copies files from one disk to another, it defragments and rearranges them during the process. Even if the external disk is mostly empty and has plenty of space to be written to, and the interface is high-speed USB 3, the transfer speeds from the internal to the external may still be slow if the internal disk is fragmented.

If the internal drive is an SSD, then although fragmentation would not substantially slow down reading from the flash (as long as it does not overheat the controller), if it is the external HDD side that is actuating to rearrange the files, then transferring files out to an HDD would be just as slow as if the internal drive was also an HDD. I have not tested to confirm if the disk being copied from or copied to is the one that actuates in order to defragment.

To obtain the true transfer speed of the external HDD with the USB 3 interface, open Command Prompt as administrator and enter <winsat disk -drive [letter]:> and then press Enter. It will display the true speed of Sequential Read and Sequential Write, without interference from the internal disk contents being defragmented in transit.