Understanding the environmental impact of bioenergy crops is needed to inform bioenergy policy development. We determined the effects of five biomass cropping systems—continuous maize (Zea mays), soybean (Glycine max)-triticale (Triticosecale ×)/soybean-maize, maize-switchgrass (Panicum virgatum), triticale/sorghum (Sorghum bicolor), and triticale-aspen (Populus alba × P. grandidentata)—on soil-saturated hydraulic conductivity (K S ) across a toposequence in central Iowa, USA. We compared data from the time of cropping system establishment in 2009 to 4 years post-establishment. Both our 2009 and 2013 data confirmed that cropping system impacts on K S vary by landscape position. We found that differences in cropping system impacts were more likely to occur at lower landscape positions, specifically, within footslope and floodplain positions. Previous research on cropping system impacts suggested that grass and woody systems were associated with a general increase in K S over time, with greater changes likely occurring at landscape positions with a higher erosive potential or lower SOC content. Our results confirmed that the triticale-aspen woody system was associated with a significant increase in K S across all landscape positions. In contrast, we did not observe an increase in K S under maize-switchgrass, which we attributed to the high density of switchgrass roots by the fourth year of study, but expect an increase in K S under switchgrass under longer measurement periods. We also found a significant increase in K S in the annual systems, likely due to the conversion to no-till soil management with cropping system establishment. We expect such differences to become more apparent over longer time scales as cropping systems continue to impact soil hydraulic properties.