Yes, to an extent, it does matter which SATA port you use. However, it also largely depends on the motherboard model and the SATA port version it features.
For instance, if you have a recent motherboard model with all the ports being SATA 3, you can use any port to connect your SATA 3 drive.
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On the other hand if you have an older motherboard with a mix of SATA 2 and SATA 3 ports, then the port you choose to connect your drive to does matter as the SATA 2 ports would have half the transfer speed as compared to the SATA 3 ports.
In addition to that, whether the SATA port matters or not also depends upon which type of storage drive you use i.e Hard Disk or SATA SSD.
Finally, on certain motherboards, some SATA ports share their connectivity with other components like the M.2 slot such that using either will disable the other.
So, does it matter which SATA port you use? Yes it does and in the text below we will talk in detail about why it does.
A Brief Overview of SATA
Image: Here you can see that the port 0, 1 (SATA3_0, SATA3_1), conform to the newer SATA 3 generation whereas the rest in the numbered order belong to the old SATA 2 generation.
So does it matter which SATA port you use? Well the answer to this question is a yes. You must consult the manual of your motherboard in order to see if there are any caveats.
There can also be instances where your motherboard has SATA ports of different generations. Though the SATA interface provides backward and forward compatibility, we recommend connecting a drive to a port of the same generation for optimal performance (for example a SATA 3 drive to a SATA 3 port on the motherboard).
As the ports vary from one motherboard model to another, finding it out through your model’s manual would give you a clear picture.