•We synthesized measured and modeling data to examine rye effects on maize systems.•Soil water deficit caused by rye transpiration affected maize yield only in drought years.•34% of the precipitation ended up in subsurface drainage at this site.•Rye produced 47kgha−1 of shoot biomass per each mm of water used.•APSIM simulated reduced NO3-N losses (26±26%), but not drainage (4±13%) or yield (2±6%). Inclusion of a rye cover crop into maize-based systems can offer environmental benefits, but adoption of the practice in the US Midwest is still low. This is related to the possible risk of reduced maize yields following rye. We hypothesized that the magnitude of rye effects on maize yields and drainage water and nitrate (NO3)-N losses would be proportionally related to rye biomass. We tested this hypothesis by analyzing data from continuous maize treatments (with and without cover crop) in Iowa, US, that were fertilized following recommendations from late spring nitrate tests. Dataset included measurements (2009–2014) of soil water and temperature, drainage water and NO3-N losses, soil NO3, rye shoot and root biomass and C:N, and maize yields. We supplemented our analysis with a literature review and the use of a cropping systems model (APSIM) to calculate trade-offs in system performance characteristics. Experimentally, rye cover crop reduced drainage by 12% and NO3-N losses by 20% (or 31% per unit of N applied), and maize yields by 6%. We also found minimal effects on soil temperature, water deficits that reduced yields only during drought years (2012 and 2013), and lower NO3-N losses that were related to reduced NO3-N concentrations in drainage. Results also revealed a linear relationship between drainage and precipitation (r2=0.96), and rye transpiration and shoot biomass (r2=0.84). Model scenario analysis (4 termination dates×30years) indicated that rye cover crop decreases NO3-N losses (-25.5±26%) but does not always reduce drainage water (-3.9±13%) or grain yields (-1.84±6%), which is consistent with experimental and literature results. However, analysis of the synthesized measured and simulated dataset do not support a strong relationship between these variables and rye biomass. These results are valuable for decision-making and add new fundamental knowledge on rye water and nitrogen use.