Pesticide residues have been linked to reduced bee health and increased honey bee colony failure. Most research to date has investigated the role of pesticides on individual honey bees, and it is still unclear how trace levels of pesticides change colony viability and productivity over seasonal time scales. To address this question we exposed standard bee colonies to chemical stressors known to have negative effects on individual bees, and measured the productivity of bee colonies across a whole year in two environments: near Tucson Arizona and Sydney Australia. We exposed hives to a trace amount of the neonicotinoid imidacloprid and to the acaricide thymol, and measured capped brood, bee and honey production, as well as the temperature and foraging force of the colonies. The effect of imidacloprid on colony dynamics differed between the two environments. In Tucson we recorded a positive effect of imidacloprid treatment on bee and brood numbers. Thymol was associated with short-term negative effects on bee numbers at both locations, and may have affected colony survival at one location. The overall benefits of thymol for the colonies were unclear. We conclude that long-term and colony-level measures of the effects of agrochemicals are needed to properly understand risks to bees.