I had six pay periods with no new York states taxes taken out, it amounted t about $3,500. I am estimating that I will make $95,000 by the end of year.

[matt723]

How will that extra money not being taken out affect my state taxes?  Will I have to pay that $3,500 back in it entirety or will it just be factored into my overall taxable income leaving it up to whatever tax bracket I fall into to decide if I owe or get a refund?

[Critter]

On the return ALL your income is reported along with ALL your withholding  and if you didn't have enough withheld to pay your tax bill then you will simply have a balance due.  If you feel you have not had enough withheld you still have 6 weeks to increase your withholding at work to make up for the short fall.

[Carl]

I don't know if NY assessed an underpayment penalty or not. But to avoid finding out the hard way you can pay estimated state taxes for NY starting at <a rel="nofollow" target="_blank" href="https://www.tax.ny.gov/pit/estimated_tax/default.htm">https://www.tax.ny.gov/pit/estimated_tax/defau...>

[Opus 17 · Accepted solution]

You owe whatever taxes you owe.  If you had insufficient withholding (for any reason) then you will owe a tax payment.  It may not be the full $3500 though.  Many people have excess tax withheld and get a refund as a result.  So the excess from the rest of the year might help cover what you owe.

The simplest thing to do is download form IT-201 from the NY tax web site and fill it out, see how much you owe.  If you are going to owe a lot, making an early estimated payment (electronically on the NY tax web site) can reduce or eliminate any late payment penalties.

Turbotax is available now if you want to buy it as a download or CD and use it to make a test return.  The online site (which would be free to make a test return but you will have to pay to actually file) won't be open for another few weeks.