Abstract The two-detector design of the NOvA neutrino oscillation experiment, in which two functionally identical detectors are exposed to an intense neutrino beam, aids in canceling leading order effects of cross-section uncertainties. However, limited knowledge of neutrino interaction cross sections still gives rise to some of the largest systematic uncertainties in current oscillation measurements. We show contemporary models of neutrino interactions to be discrepant with data from NOvA, consistent with discrepancies seen in other experiments. Adjustments to neutrino interaction models in GENIE are presented, creating an effective model that improves agreement with our data. We also describe systematic uncertainties on these models, including uncertainties on multi-nucleon interactions from a newly developed procedure using NOvA near detector data.