Roots of Canada thistle were excavated from the soil monthly from 1999 to 2001 near Scottsbluff, NE, to quantify the influence of changing soil temperature on free sugars and fructans in roots. Sucrose concentrations were low from May through August then increased in the fall and remained at high levels during winter and then declined in April as plants initiated spring growth. Changes in sucrose, 1-kestose (DP 3) and 1-nystose (DP 4) were shown to be closely associated with changes in soil temperature. During the second year of the study, average soil temperatures during the winter were colder than the first year and resulted in an increase of sucrose in Canada thistle roots. Experiments were conducted from 2001 to 2004 to determine whether there was a correlation between herbicide efficacy, time of herbicide application, and the resulting herbicide effect on root carbohydrate and Canada thistle control. Clopyralid applied in the fall reduced Canada thistle density 92% 8 months after treatment (MAT) whereas treatment made in the spring reduced plant density 33% 11 MAT. Fall application of clopyralid increased the activity of fructan 1-exohydrolase (1-FEH) in roots and was associated with a decline in sucrose, DP 4, and 1-fructofuranosyl-nystose (DP 5) 35 d after treatment (DAT). Spring application of clopyralid also resulted in a decrease of the same carbohydrates 35 DAT, but by 98 DAT, or early October, sucrose level in roots had recovered and was similar to nontreated plants. Fall application of 2,4-D or clopyralid reduced Canada thistle density 39 and 92% respectively, 8 MAT, but only clopyralid resulted in a reduction of sucrose, DP 4, DP 5, and total sugar and an increase of 1-FEH compared with nontreated plants.