With public focus on sustainable food production, cover crops (CC) integration into production systems is encouraged to improve soil structure; however, the effects of herbicide residues on the ability of CC to improve soil aggregation and fertility are poorly understood. In spring of 2012 and 2013, saflufenacil/dimethenamid-p (735,1470 g a.i.ha-1) and s-metolachlor/atrazine+mesotrione (2880+140 and 5760+280 g a.i.ha-1) were applied preemergence (PRE) to sweet corn, and imazethapyr (100,200 g a.i.ha-1) was applied PRE to pea. Fall-seeded CC: rye (Secale cereale L.), hairy vetch (Vicia villosa Roth.), oilseed radish (Raphanus sativus L. var. oleiferus), and oat (Avena sativa L.) and spring-seeded CC: ryegrass (Lolium multiflorum L.), buckwheat (Fagopyrum esculentum Moench.), sorghum-sudangrass (Sorghum bicolor x Sorghum bicolor L. var. sudanese) and wheat (Triticum aestivum L.) were sown four months (fall) and a year (spring) vertically into herbicide treatments and untreated-control (horizontal plots). We hypothesized CC root biomass and consequently N immobilization, aggregate size and stability would decrease in herbicide treatments compared to untreated-check. Herbicide effect on CC root biomass and N content, mineral N (SMN), wet aggregate stability (WAS) and aggregate size was determined before main (BMCS) and CC seeding (BCCS). Roots biomass decreased in buckwheat, sorghum-sudangrass, vetch and radish after imazethapyr; in ryegrass, buckwheat and oilseed-radish after s-metolachlor/atrazine+mesotrione applications and in radish; and vetch after saflufenacil/dimethenamid-p (2X). SMN was similar among treatments in the spring but greater in fall-BCCS imazethapyr treatments. Aggregate size was similar among treatments in spring-planted CC but differed among winterkilled and winter-hardy CC in the fall. WAS increased in the spring-BCCS, in imazethapyr and s-metolachlor/atrazine+mesotrione treatments and in the fall-BMCS, in saflufenacil/dimethenamid-p as well as oat-seeded plots. Additionally, sugarbeet (Beta vulgaris L.) greenhouse bioassays were conducted using soil samples collected from all herbicide x CC combinations. Hypothesis was sugarbeet injury would be greater in PRE herbicide-applied soils than in untreated soil, and response depended on CC species previously seeded herbicide treatments. None of the CC reduced herbicide injury to sugarbeet. Overall, herbicide residues reduced CC roots and root N, and subsequently impacted soil parameters studied. Furthermore, CC roots have no influence in herbicide dissipation rates in the soil.