This study aimed to determine genotype and environment effects on the yield and selected quality traits of winter rye from organic production. The tested material was grain of two hybrid rye cultivars, Tur and KWS Dolaro, and five population cultivars of rye, Dańkowskie Hadron, Dańkowskie Granat, Dańkowskie Turkus, Dańkowskie Skand, and Piastowskie. Field trials were performed at two locations in Poland, Osiny and Grabów, in two growing seasons, 2018/2019 and 2019/2020. The grain yield, moisture content, falling number, thousand-grain weight, and hectoliter weight were determined. The content of basic nutrients, protein, minerals, lipids, carbohydrates, and dietary fibre, as well as the viscosity of aqueous extracts of grain, were also determined. This study revealed that environmental factors, such as harvest year and growing location, as well as the genotype factor, had the greatest effect on the viscosity of aqueous extracts and protein content. The study’s hybrid cultivars, Tur and KWS Dolaro, are characterized by significantly higher yield but lower dietary fibre and protein contents in rye grain and lower viscosity of aqueous compared to all study population cultivars. Of all the studied population cultivars of rye, the grain of the cultivar Dańkowskie Skand was found to be the most beneficial in terms of nutritional value because it was characterized by the highest viscosity of aqueous extracts.