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Your best course of action is to contact (1-800-959-8281) CRA directly about your situation, but I can share the tax rules that apply. 

Under the federal Income Tax Act, common-law couples are treated the same as married couples. The definition of a common-law partner under the Act is: “A person with whom you live in a conjugal relationship who is not your spouse, and he or she:

• has been living with you at least 12 continuous months (includes any period you were separated for less than 90 days because of a breakdown in the relationship); OR
• is the parent of your child by birth or adoption; OR
• has custody and control of your child (or had custody and control immediately before the child turned 19 years of age) and your child is wholly dependent on that person for support.”

Effects of filing tax as a common-law partner:

• While you may be able to maximize certain tax credits and deductions when filing as a common-law partner, you may also lose some tax credits you might have been entitled to when filing as a single person because your combined income makes you ineligible. Or, only one partner will be eligible to receive the benefit.

Credits and benefits that you may lose include:

• the eligible dependant credit, which one or both partners may be claiming if they are raising a child,
• the Guaranteed Income Supplement (GIS) and the Allowance (offered under the Old Age Security Program). 
• the GST/HST credit, and
• the Canada Child Benefit (CCB). 

The following Marital Status doesn't apply to you:

1. Separated means that you have been living apart from your spouse or common-law partner because of a breakdown in the relationship for a period of at least 90 days.

2. Widowed means that you had a spouse or common-law partner who is now deceased.

3. Divorced means that you are legally divorced from your former spouse.

4. Single means that none of the other marital statuses applies to you.

Bottom line - if you are living as a common-law couple, you should file as one as you are also living together during "separation".

For more information, please visit Canada Revenue Agency's website: Marital Status.

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