An important but rarely studied aspect of crop modeling is the uncertainty associated with model calibration and its effect on model prediction. Biomass and grain yield data from a four-year maize experiment (2008–2011) with six irrigation treatments were divided into subsets by either treatments (Calibration-by-Treatment) or years (Calibration-by-Year). These subsets were then used to calibrate crop cultivar parameters in CERES (Crop Environment Resource Synthesis)-Maize implemented within RZWQM2 (Root Zone Water Quality Model 2) using the automatic Parameter ESTimation (PEST) algorithm to explore model calibration uncertainties. After calibration for each subset, PEST also generated 300 cultivar parameter sets by assuming a normal distribution of each parameter within their reported values in the literature, using the Latin hypercube sampling (LHS) method. The parameter sets that produced similar goodness of fit (11–164 depending on subset used for calibration) were then used to predict all the treatments and years of the entire dataset. Our results showed that the selection of calibration datasets greatly affected the calibrated crop parameters and their uncertainty, as well as prediction uncertainty of grain yield and biomass. The high variability in model prediction of grain yield and biomass among the six (Calibration-by-Treatment) or the four (Calibration-by-Year) scenarios indicated that parameter uncertainty should be considered in calibrating CERES-Maize with grain yield and biomass data from different irrigation treatments, and model predictions should be provided with confidence intervals.

To help reduce future N loads entering the Gulf of Mexico from the Mississippi River 45%, Iowa set the goal of reducing non-point source N loads 41%. Studies show that implementing winter rye cover crops into agricultural systems reduces N loads from subsurface drainage, but its effectiveness in the Mississippi River Basin under expected climate change is uncertain. We used the field-tested Root Zone Water Quality Model (RZWQM) to estimate drainage N loads, crop yield, and rye growth in central Iowa corn-soybean rotations. RZWQM scenarios included baseline (BL) observed weather (1991–2011) and ambient CO₂ with cover crop and no cover crop treatments (BL_CC and BL_NCC). Scenarios also included projected future temperature and precipitation change (2065–2085) from six general circulation models (GCMs) and elevated CO₂ with cover crop and no cover crop treatments (CC and NCC). Average annual drainage N loads under NCC, BL_NCC, CC and BL_CC were 63.6, 47.5, 17.0, and 18.9 kg N ha⁻¹. Winter rye cover crop was more effective at reducing drainage N losses under climate change than under baseline conditions (73 and 60% for future and baseline climate), mostly because the projected temperatures and atmospheric CO₂ resulted in greater rye growth and crop N uptake. Annual CC drainage N loads were reduced compared with BL_NCC more than the targeted 41% for 18 to 20 years of the 21-year simulation, depending on the GCM. Under projected climate change, average annual simulated crop yield differences between scenarios with and without winter rye were approximately 0.1 Mg ha⁻¹. These results suggest that implementing winter rye cover crop in a corn-soybean rotation effectively addresses the goal of drainage N load reduction under climate change in a northern Mississippi River Basin agricultural system without affecting cash crop production.