Modern versions of Windows, Linux, and Mac OS all have built-in utilities to completely encrypt the contents of your hard drives. Use these tools. Many people don’t encrypt their drives because they believe they have nothing to hide. But encryption your drive also protects against individuals altering the contents on your drive. This can be very valuable.
While an operating system will attempt to prevent unauthorized users from altering files or installing software when it has been booted by it will be rendered powerless if another method is used to boot the system, such as a boot disk. An encrypted hard drive, on the other hand, cannot be written to (any alteration of the encrypted data will appear to be garbage when you attempt to decrypt the drive) unless it is decrypted with the appropriate key.
That means an encrypted disk will prevent an attacker with physical access from installing software keyloggers, rootkits, and other potentially troublesome forms of malicious software.
I spent a decent portion of last night helping somebody deal with this scenario. As a related side note if you suspect your jealous and/or abusive significant other of having installed surveillance software on your system feel free to contact me. I will provide what assistance I can and I won’t charge a dime.