Canada thistle is a serious perennial weed found throughout the northern regions of the United States and Canada. The weevil, Ceutorhynchus litura (F.), was first released in Canada in 1965 as a potential biological control agent for Canada thistle; however, its impact as a control agent has been sporadic. The objective of this study was to characterize C. litura impacts on the carbohydrate profile in Canada thistle roots through the growing season and to evaluate the potential for this biological control agent in causing stress to Canada thistle. Field plots, infested with C. litura, were established and extensively sampled for C. litura infestations. By sampling C. litura–damaged and undamaged Canada thistle shoots–roots through the season, we were able to establish the profile of free sugars and fructans in the roots and compare these levels to the presence and extent of insect damage. Levels of all free sugars and fructans were consistently found to be depressed in roots from C. litura–damaged shoots early in the summer during and shortly after the larval feeding period. Ceutorhynchus litura feeding in Canada thistle shoots appears to disrupt the movement of photoassimilates from leaves to roots. Late-season levels of free sugars and fructans indicate that roots do recover from these depressed levels, and in several instances, significant overcompensation occurred in the damaged roots. Measurement of free sugars and fructans to identify sublethal impacts of control tactics may allow the strategic combining of complementary tactics to maximize the impact of stresses on Canada thistle.