Cover crop (CC) prevalence between cash crop systems is contributing to long-term sustainable crop production systems. However, herbicide residue impact on CC root growth and its subsequent effect on soil aggregation and fertility are unknown. An untreated control plus preemergence (PRE) application of saflufenacil (at 67 and 134 g a.i. ha^-1)/dimethenamid-P (at 668 and 1336 g a.i. ha^-1) as well as S-metolachlor (at 1600 and 3200 g a.i. ha^-1)/atrazine (at 1280 and 2560 g a.i. ha^-1) + mesotrione at 140 and 280 g a.i. ha^-1 to sweet corn (Zea mays L. var. rugosa Bonaf.) and imazethapyr (100 and 200 g a.i. ha^-1) to pea (Pisum sativum L.) were made in spring 2011 and spring 2012. One year later, ryegrass (Lolium multiflorum Lam.), buckwheat (Fagopyrum esculentum Moench), sorghum–sudangrass [Sorghum bicolor (L.) Moench × S. bicolor var. sudanese (L.)], and spring wheat (Triticum aestivum L.) were seeded. Root biomass and N content, wet aggregate stability (WAS), and aggregate size plus soil mineral N (SMN) were determined. Buckwheat root biomass declined in all herbicide treatments but root N declined in imazethapyr and S-metolachlor/atrazine + mesotrione at the 2× and 1× rates, respectively. Ryegrass root biomass decreased in S-metolachlor/atrazine + mesotrione but root N content declined only at the 2× rate. Sorghum–sudangrass and spring wheat roots decreased in imazethapyr and S-metolachlor/atrazine + mesotrione at the 2× rate, respectively. Despite the impact of herbicide residues on roots, differences in aggregate size, WAS, and SMN were not detected. Findings from this study add knowledge on herbicide residue effect on CC root growth and provide useful CC seeding guidelines for growers.