In rolling landscapes, plant available water varies drastically by location.  Almost simultaneously, plants may be flooded out in footslope locations whereas plants in summit locations may be suffering from severe drought.  To understand the effects of water-limiting conditions on plant growth and, ultimately, gene expression, corn was sampled at V12 for plant growth characteristics and transcriptome analysis at summit (drought conditions) and toeslope (adequate water conditions) positions. Plants at the summit had 16% less leaf area and biomass compared with plants at the toeslope.  Gene expression analysis using microarray chips, transcriptome analysis, and qPCR indicated that plants at the summit had 708 genes down-regulated and 399 genes up-regulated compared to control plants at the toeslope. GSEA (Gene Set Enrichment Analysis) indicated tolerance to cold, salt, and drying were increased in summit plants compared to control toeslope plants. However, nutrient uptake, recovery from wounding, pest and fungal disease resistance, along with photosynthetic capacity were all down-regulated in summit plants. Numerous genes associated with circadian rhythm were down-regulated in summit plants, potentially having a profound effect on flowering, growth, and nutrient uptake.  Overall, transcriptome analysis indicated that the combination of drought and landscape position can greatly diminish the plants ability to withstand and recover from pests.