Characterizing the natural diversity of gene expression across environments is an important step in understanding how genotype by environment interactions shape phenotypes. Here, we analyzed the impact of water deficit onto gene expression levels in tomato at the genome-wide scale. We sequenced the transcriptome of growing leaves and fruit pericarps at cell expansion stage in a cherry and a large fruited accession and their F1 hybrid grown under two watering regimes. Gene expression levels were steadily affected by the genotype and the watering regime. Whereas phenotypes showed mostly additive inheritance, ~80% of the genes displayed non-additive inheritance. By comparing allele specific expression in the F1 hybrid to the allelic expression in both parental lines, respectively, 3,005 genes in leaf and 2,857 genes in fruit deviated from 1:1 ratio independently of the watering regime. Among these genes, ~55% were controlled by cis factors, ~25% by trans factors and ~20% by a combination of both types. A total of 328 genes in leaf and 113 in fruit exhibited significant allele specific expression by watering regime interaction, among which ~80% presented trans by watering regime interaction suggesting a response to water deficit mediated through a majority of trans acting loci in tomato. We cross-validated the expression levels of 274 transcripts in fruit and leaves of 124 RILs and identified 163 eQTLs mostly confirming the divergences identified by allele specific expression. Combining phenotypic and expression data, we observed a complex network of variation between genes encoding enzymes involved in the sugar metabolism.