Volatile organic compounds (VOCs) are responsible for flavour development in watermelon (Citrullus lanatus). The objective of this study was to investigate the rootstock effects of 21 local bottle gourd [Lagenaria siceraria (Molina) Standl.] accessions collected from the Mediterranean region (Turkey) on the concentrations of VOCs in watermelon over 2 years. The watermelon cultivar 'Crimson Tide' was used as the scion and two commercial bottle gourd rootstocks were also used for comparison. The VOCs in each rootstock-scion combination were analysed using static headspace (SHS) and gas chromatography-mass spectrometry (GC-MS). A total of 24 VOCs were identified in watermelon fruit, including 11 aldehydes, seven alcohols, four ketones, one heterocyclic compound, and one acid. Acetaldehyde (25.9 - 39.5% of the total peak areas), propanal (5.0 - 8.3%), 2-propanone (2.5 - 4.9%), pentanal (2.1 - 3.6%), hexenal (14.5 - 22.6%), (E)-2-hexenal (0.4 - 2.3%), 6-methyl-5-hepten-2-one (10.0 - 19.05%), nonanal (1.6 - 4.4%), (Z)-6-nonenal (4.0 - 9.8%), (E)-2-nonenal (0.6 - 2.0%), (E,Z)-2,6-nonadienal (2.1 - 3.7%), (Z)-6-nonenol (1.0 - 3.2%), and (E,Z)-3,6-nonadienol (1.0 - 3.7%) were the most abundant VOCs found in all watermelon scions. There was no significant effect (P >= 0.05) of rootstock on the concentrations of acetaldehyde, propanal, pentanal, heptanal, ethanol, 1-pentanol, 2-propanone, 2-pentyl furan, or acetic acid. Propanal, 2-propanone, and acetic acid were identified as VOCs in watermelon for the first time. Hexanal, (Z)-6-nonanal, and 6-methyl-5-hepten-2-one concentrations were strongly affected by rootstock. The results showed that the local bottle gourd accessions 07-06 and 31-09, in particular, were the most promising genotypes in terms of producing favourable VOCs. Except for the local bottle gourd accessions 33-35, 01-17, and 07-04, the other 18 gourds accessions had high potential as rootstocks for breeding programmes in watermelon with regard to desirable VOC concentrations. Rootstock 31-09 should be considered for commercial production in terms of improved disease resistance, fruit yield, and fruit quality.