A field experiment was conducted from 1994 to 2013 at Scott, SK, to assess the effects of cropping diversity and inputs on spring wheat, canola, and barley yield in the context of growing season precipitation (GSP), growing degree days (GDD), and terrain attributes. Main-plot treatments consisted of three levels of agricultural inputs [organic (ORG), reduced (RED), and high (HI)] and sub-plot treatments consisted of three levels of cropping diversity [low (LOW), diversified annual grains (DAG), and diversified annual perennial]. Yield was highest for the HI and RED inputs, and lower for the ORG system. The HI–DAG, HI–LOW, RED–DAG, and RED–LOW rotations produced the highest yields. April precipitation was identified as a primary yield-driving factor in this study. April precipitation and fixed effects accounted for up to 22% and 10% of yield variation, respectively, in analyses by 6-yr periods. Terrain attributes explained up to 4.5% of variation in annual yield. The effects of inputs and diversity on crop yield were influenced by GSP, GDD, and terrain attributes and show the importance of crop management in the context of environmental variability.