Sixty commercial honey bee colonies were monitored over the course of one year with the goal of assessing potential correlations between measured colony strength and environmental stressors, including exposures to pesticides and pathogens. We developed a new method for assessing colony health by determining the fractional change in population of the four colonies on each pallet between peak population on 1 June and the last population assessment prior to winter on 1 October. This fractional change in population was evaluated as a function of pesticide load per pallet for each of the 37 pesticide chemicals detected, grouping pallets by beekeeper. The analysis of individual chemicals showed that both imidacloprid and cyprodinil were negatively correlated with colony health, while tau-fluvalinate and dinotefuran (at very low concentrations) were positively correlated, possibly because of effects on Varroa control. Exposure to groups of chemicals was also evaluated. Normalization of each chemical concentration to the maximum observed for that chemical provided an equal weighting for each chemical, even though their relative occurrence in the environment and their effective toxicities might differ. A total of 24 chemical groups whose members share a structural commonality, a functional commonality, or suspected synergistic actions were considered, demonstrating negative correlations between colony health and exposures to neonicotinoids as a group and neonicotinoids in combination with (1) methoxyfenozide (2) organophosphates, and (3) diflubenzuron. Analysis of several groups of fungicides applied to almonds during pollination also showed negative correlations with colony health.