Flaxseed (Linum usitatissimum L.) is a plant with a wide range of medicinal, health, nutritional, and industrial uses. This study assessed the genetic potential of yellow and brown seeds in thirty F4 families under different water conditions concerning seed yield, oil, protein, fiber, mucilage, and lignans content. Water stress negatively affected seed and oil yield, while it positively affected mucilage, protein, lignans, and fiber content. The total mean comparison showed that under normal moisture conditions, seed yield (209.87 g/m²) and most quality traits, including oil (30.97%), secoisolariciresinol diglucoside (13.89 mg/g), amino acids such as arginine (1.17%) and histidine (1.95%), and mucilage (9.57 g/100 g) were higher in yellow-seeded genotypes than the brown ones ((188.78 g/m²), (30.10%), (11.66 mg/g), (0.62%), (1.87%), and (9.35 g/100 g), respectively). Under water stress conditions, brown-seeded genotypes had a higher amount of fiber (16.74%), seed yield (140.04 g/m²), protein (239.02 mg. g⁻¹), methionine (5.04%), and secondary metabolites such as secoisolariciresinol diglucoside (17.09 mg/g), while their amounts in families with yellow seeds were 14.79%, 117.33 g/m², 217.12 mg. g⁻¹, 4.34%, and 13.98 mg/g, respectively. Based on the intended food goals, different seed color genotypes may be appropriate for cultivation under different moisture environments.