Honey bee is battling an acute population decline. Research efforts to identify the culprit pinpoint to a multifactorial etiology entailing a mitigation approach that adopts an integrated analysis of stressors at local levels. In this research, a holistic survey of diseases, pesticide residues, and stored-pollen quality is conducted in fall (2022), spring (2023), and summer (2023) throughout all 6 geographical regions of Kentucky. To achieve these objectives, we performed a seasonal collection of hive matrices (bees, pollen, wax, and honey) from 10 apiaries per region and 5 hives per apiary. The sampled hives were also assessed for colony strength and ranked as strong, moderate, or weak. For the diagnosis and discovery of diseases the bee samples were analyzed via RNA-seq, while the pollen samples were examined for the presence of over a hundred pesticides and subjected to a metagenomics analysis for species identifications. An epidemiological pilot survey using a questionnaire assessing colony management and winter colony losses was given to all beekeepers included in the sampling. This multifaceted research is being conducted to uncover possible correlations of disease prevalence, pesticide contaminations and food quality with colony strength. The systematic seasonal and regional sampling will capture the variations in disease, pesticide residues, and pollen quality throughout Kentucky landscape. The epidemiological pilot survey assessing overwintering losses and colony management will be used for a larger survey of hundreds of beekeepers throughout Kentucky. The results of such comprehensive study will be useful in outreach efforts to promote colony health in Kentucky.