Watermelon fruit [Citrullus lanatus (Thumb) Matsum & Nakai] is a natural source of phytonutrients, including lycopene, citrulline, and arginine. Two segregating, highly outcrossed North Carolina watermelon populations, NC High Yield (NCHYW) and NC Small Fruit (NCSFW), were evaluated for these traits and for indicators of ripeness (pH and soluble solids content). Parents tested in 2015 (NSF = 300, NHY = 300) were sampled for the above and offspring were tested in 2016 if the sampled fruit of the parents were of qualifying ripeness [soluble solids concentration (SSC) ≥8, pH 5.5–6.5], resulting in 251 families (NSF = 72, NHY = 175). Narrow-sense heritability was estimated in each of the populations using the methods of 1) parent-offspring regression and 2) variance of half-sibling family means. Heritability for citrulline in NCHYW was moderate in both parent-offspring and half-sibling estimations (38% and 43%), as was arginine (40% and 44%) and lycopene (46% and 47%, respectively). Estimates for these traits in NCSFW were considerably different, with parent-offspring and half-sibling estimations for citrulline (65% and 22%), arginine (9% and 20%), and lycopene (44% and 68%). In NCHYW, moderate phenotypic correlations were found between SSC and citrulline (0.40), arginine (0.40), their combination (0.45), and lycopene (0.30) all of which were significant, except lycopene. Lycopene was significantly and weakly correlated to citrulline (0.22), but was not correlated to arginine (0.06). Similar correlations were found in NCSFW; SSC was significantly correlated to citrulline (0.24), arginine (0.18), and their combination (0.23), whereas lycopene was slightly correlated to citrulline (0.15) and not significantly correlated to arginine. Based on these heritabilities and phenotypic correlations, tandem selection for high lycopene and citrulline content may be accomplished efficiently using progeny rows with minimal replication using the NCSFW population, whereas replication with multiple years, rows, and locations may be necessary for creating stable lines using the NCHYW population.