Spectra of natural sunlight and artificial sources are important in photovoltaic research. Calibration of the spectroradiometers used for these measurements is derived from the response to spectral irradiance standards from the National Institute of Standards and Technology (NIST). Some photovoltaic devices respond in the near infrared, or NIR, so spectral measurements and calibrations are needed in this region. Over the course of several calibrations, we identified variations > 5% in spectroradiometer NIR calibration data for a certain spectroradiometer. A detailed uncertainty analysis did not reflect the observed variation. Reviewing calibration procedures and historical data, we noted that the variations were seen in water vapor absorption bands. We used spectral transmission models to compute changes in atmospheric transmission (as a function of water vapor content) over path lengths occurring during calibration. The results indicate that the observed variations result from varying water vapor content. A correction algorithm for adjusting measured data was developed based on our analysis.