No, they won't be much isolated.
Each install will be isolated from a normal usage. For instance, a Windows update installed on one Windows, won't be applied to the other.
The main problem, as hinted by Rory Aslop, is that both will be able to see each other partition. So a virus which eg. infected each
.exe files on the computer, will infect both installs.
This is often not the case if you had disparate OS. Windows 98 won't be able to read a Windows 8 install, nor will Windows 8 read a Linux filesystem.¹ Thus, it would be much harder that a virus on the former affects the later, although not impossible: remember that there's no physical separation. The virus could include a driver for the other filesystem, it could search the raw disk for the files to infect or, more simple, just wipe the full disk.
As you seem to want them isolated one another, I would make the partition of the OS-not-currently-booted hidden / unassign its drive letter, so a malware would at least need to mount it in order to access there, as opposed to simply infect all mounted drives.
¹ Note that the reverse is often not true.