Is there a way to have separate passwords to access docs I have stored in separate folders?
You can password protect each Share via the WD My Cloud Dashboard. If you have not already done so it is recommended one read the My Cloud User Manual which explains how to setup Users and then configure a Share to Private and apply user permissions (Full Access, Read Access, No Access) to that Share. The Help within the My Cloud Dashboard also explains how to configure a Share to Private and setup Users for access to that Share.
Bennor is correct, unless you have a domain controller in your house (i.e. Win 2008 or Win 2012) where you can grant NTFS permissions by user or group to individual folders under a top level share.
Aside from that, no.