The Moderate Resolution Imaging Spectroradiometer (MODIS) is currently flying on both the Terra and Aqua satellite platforms. The Ocean Biology Processing Group (OBPG) at NASA Goddard Space Flight Center is producing operational ocean color products from the MODIS-Aqua sensor; however, documented uncertainties and instabilities in the prelaunch and on-orbit characterization have inhibited the production of similar products from MODIS-Terra. In particular, the radiometric response of the 412-nm band has degraded by more than 40% over the 7-year mission lifespan, with similar though less extreme changes in the longer wavelengths. While such variability may be fully correctable through the on-board calibration system, it suggests that the optical properties of the scan mirror have changed significantly since launch. Furthermore, the degradation trends are substantially different between the two mirror sides, which is likely a result of asymmetric damage done to the mirror during prelaunch testing. These effects contribute to uncertainty in our knowledge of instrument response versus incidence angle on the mirror and sensitivity with respect to polarization of the observed radiance. In this paper, we examine the impact of apparent MODIS-Terra instrument characterization errors on the derived ocean color products and show that residual errors in the current operational calibration give rise to significant cross-scan artifacts, mirror-side differences, and detector-to-detector striping in the retrieved water-leaving radiances. In addition, we describe OBPG efforts to reduce these artifacts through statistical and vicarious instrument characterization, and show the quality of the resulting water-leaving radiance retrievals relative to those derived from MODIS-Aqua.