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Abstract Soybean (Glycine max[L.] Merr.) production is susceptible to biotic and abiotic stresses, exacerbated by extreme weather events. Water limiting stress, that is, drought, emerges as a significant risk for soybean production, underscoring the need for advancements in stress monitoring for crop breeding and production. This project combined multi‐modal information to identify the most effective and efficient automated methods to study drought response. We investigated a set of diverse soybean accessions using multiple sensors in a time series high‐throughput phenotyping manner to: (1) develop a pipeline for rapid classification of soybean drought stress symptoms, and (2) investigate methods for early detection of drought stress. We utilized high‐throughput time‐series phenotyping using unmanned aerial vehicles and sensors in conjunction with machine learning analytics, which offered a swift and efficient means of phenotyping. The visible bands were most effective in classifying the severity of canopy wilting stress after symptom emergence. Non‐visual bands in the near‐infrared region and short‐wave infrared region contribute to the differentiation of susceptible and tolerant soybean accessions prior to visual symptom development. We report pre‐visual detection of soybean wilting using a combination of different vegetation indices and spectral bands, especially in the red‐edge. These results can contribute to early stress detection methodologies and rapid classification of drought responses for breeding and production applications.