The temporal control of gene expression leads to time of day effects on metabolism and physiology. To identify early transcript level changes occurring in the Brassica rapa oil-type variety R500 during initial drought perception we performed an RNA-seq time course experiment. Leaf tissue was collected from well-watered and drought treated 18 day old plants grown under 14h light at 22째C/10h dark at 18째C every 4h over 2 days with 2 biological replicates at every time point. We collected physiology measurements at every time point and observed dynamic time of day changes in photosynthetic rate, stomatal conductance, non-structural carbohydrates and PSII efficiency. Using a co-expression network approach, phase dependent gene modules were correlated with the physiology data to reveal temporally regulated drought responses. This study provides insight into the transcriptome level responses occurring in the plant in the early stages of drought perception before visible signs of stress occur. Overall design: Brassica rapa subsp. trilocularis (R500) plants were grown under 14h light at 22째C and 10h dark at 18째C for 16 days after sowing (DAS) before water was withheld from half the plants. Starting at 18 DAS leaf tissue was collected from well-watered and droughted plants every 4 h for 2 days starting 1h after dawn. We collected 2 replicates for every time point.