Continued increases in nitrogen and phosphorus loads in waterways cause problems with water quality, impacting human health, the economy, and the environment. To reach nutrient load reduction targets, innovative conservation strategies should be evaluated. This study used oval mesocosms (1.2 m × 0.58 m × 0.58 m) to assess the (1) potential of using woodchip‐bioditch reactors for the mitigation of nitrate (NO3−) and soluble reactive phosphorus (SRP) in agricultural waterways; (2) influence of bioditch reactor orientation (parallel, perpendicular, and hybrid) to flow direction on NO3− and SRP concentrations and loads; and (3) impact of bioditch reactor saturation (dry, intermittently wet, and wet) on NO3− and SRP loads reduction. Woodchip‐bioditch reactors successfully reduced NO3− loads compared to controls (p ⩽ 0.031), but SRP load was sometimes higher in bioditch reactor treatments. No consistent differences were identified between orientation of bioditch reactors and flow direction. The constantly wet treatment had a significantly higher NO3− load reduction than the dry treatment and control (p ⩽ 0.042). Our results indicate the promise of woodchip‐bioditch reactors as a nutrient reduction conservation strategy, although further study of nutrient and greenhouse gas dynamics is needed before widespread implementation.