Why Do I Owe State Taxes But Not Federal

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If you owe state taxes but are getting a federal refund, can those funds be used to make the payment? I know NY is an efile Now, if you 're using the Refund Processing Service, you can pay your TurboTax state preparation fee with your federal refund - just not your state tax bill. owed. How do I make my payment to you?.If you finish your tax return and are confused as to why you need to send the IRS a check, there is only one possible explanation for this: you paid less tax during the year than you owed for your income level. The more allowances you report on your W-4, the less tax that is withheld from your paycheck..