Conservation practices are designed and implemented to reduce soil erosion and protect water quality, but their effectiveness has been found to vary widely. This study investigated spatial and temporal variability in sediment and nutrient loads and load reductions achieved by implementing conservation practices to understand the implications of landscape heterogeneity and seasonal land-phase hydrologic variation on the effectiveness of the practices. Field-scale effects of nine conservation practices were evaluated in an agricultural watershed in the Midwest using the SWAT model. Results show that the conservation practice effectiveness, and the variability of the practice effectiveness at different locations, vary widely. Most practices are more effective in reducing nutrients in particulate than soluble forms. Practices applied to fields with higher nutrient loads do not necessarily lead to greater load reduction, indicating that an assumption of a proportional relationship between load and expected load reduction on which common targeting strategies for conservation practice placement are based may not be valid for nutrient, in particular soluble forms. The variation ineffectiveness of the practices varied substantially by fields and seasons, suggests that achievement of water quality improvement requires careful selection of conservation practices and target areas considering hydrologic variations.