Simple SummaryThe number of honey bee, Apis mellifera L., colonies has reduced around the globe, and one potential cause is their unintended exposure to sublethal stressors such as agricultural pesticides. The quantification of such effects at colony level is a very complex task due to the innumerable collective activities done by the individual within colonies. Here, we present a Bayesian and computational approach capable of tracking the movements of bees within colonies, which allows the comparison of the collective activities of colonies that received bees previously exposed to uncontaminated diets or to diets containing sublethal concentrations of an agricultural pesticide (a commercial formulation containing the synthetic fungicides thiophanate-methyl and chlorothalonil). Our Bayesian tracking technique proved successful and superior to comparable algorithms, allowing the estimation of dynamical parameters such as entropy and kinetic energy. Our efforts demonstrated that fungicide-contaminated colonies behaved differently from uncontaminated colonies, as the former exhibited anticipated collective activities in peripheral hive areas and had reduced swarm entropy and kinetic energies. Such findings may facilitate the electronic monitoring of potential unintended effects in social pollinators, at colony level, mediated by environmental stressors (e.g., pesticides, electromagnetic fields, noise, and light intensities) alone or in combination.Interactive movements of bees facilitate the division and organization of collective tasks, notably when they need to face internal or external environmental challenges. Here, we present a Bayesian and computational approach to track the movement of several honey bee, Apis mellifera, workers at colony level. We applied algorithms that combined tracking and Kernel Density Estimation (KDE), allowing measurements of entropy and Probability Distribution Function (PDF) of the motion of tracked organisms. We placed approximately 200 recently emerged and labeled bees inside an experimental colony, which consists of a mated queen, approximately 1000 bees, and a naturally occurring beehive background. Before release, labeled bees were fed for one hour with uncontaminated diets or diets containing a commercial mixture of synthetic fungicides (thiophanate-methyl and chlorothalonil). The colonies were filmed (12 min) at the 1st hour, 5th and 10th days after the bees’ release. Our results revealed that the algorithm tracked the labeled bees with great accuracy. Pesticide-contaminated colonies showed anticipated collective activities in peripheral hive areas, far from the brood area, and exhibited reduced swarm entropy and energy values when compared to uncontaminated colonies. Collectively, our approach opens novel possibilities to quantify and predict potential alterations mediated by pollutants (e.g., pesticides) at the bee colony-level.