Citrulline, arginine, and lycopene are naturally occurring compounds found in watermelon, Citrullus lanatus (Thumb) Matsum & Nakai, with beneficial effects on plant growth and human health. This study evaluated seven commercial cultivars and one breeding line for citrulline, arginine, and lycopene content in mature fruit grown at two locations in North Carolina. Correlations among these compounds and fruit quality traits (percent soluble solids and flesh pH) were evaluated. Watermelon cultigens evaluated were chosen for their fruit trait diversity. ‘Yellow Doll’ and NC-517 possessed the highest citrulline and combined concentration of citrulline and arginine of all cultigens evaluated. Lycopene content was highest in ‘Dixielee’, followed by ‘Sugar Baby’, and ‘Allsweet’, each of which have different shades of red flesh color. Location and its interaction with genotype had no significant effect on arginine or lycopene concentration. Broad-sense heritability was estimated for each trait. Arginine content (89%) and lycopene content (99%) had very high heritability. Citrulline content (41%), percent soluble solids (46%), and flesh pH (61%) had moderate heritability. Lycopene was positively correlated with flesh pH (r = 0.517) and negatively correlated with percent soluble solids (r = −0.344). Arginine content had a weak negative correlation with flesh pH (r = −0.343) and was not correlated with percent soluble solids.