The aim of this study was to evaluate the influence of rye genotype, harvest year, and growing location on the chemical composition and baking quality of rye flour (55% extraction rate). Flours were produced from five population cultivars and two hybrid cultivars, cultivated in two locations in Poland, Osiny and Grabów, during the 2018/2019 and 2019/2020 seasons under organic farming conditions. Basic chemical composition (lipids, minerals, protein, carbohydrates), dietary fiber and its fractions (non-starch polysaccharides and lignin), and water extract viscosity were determined. Baking quality was assessed using falling number and water absorption. The results showed that harvest year exerted the strongest effect on rye flour properties. Flour produced from grain harvested in 2019 contained higher levels of protein (7.9% d.m.), lipids (0.74% d.m.), nutrition compounds, and falling number (297 s) but lower water absorption (63.3%). Rye flour samples from the 2020 harvest had a higher proportion of soluble fractions, which increased water extract viscosity. Among the cultivars, Dańkowskie Skand demonstrated the most favorable baking characteristics, with the lowest falling number (271 s) and the highest water absorption (65.5%). The most advantageous chemical components were observed in Dańkowskie Hadron flour due to its high contents of dietary fiber (7.47% d.m.), non-starch polysaccharides (6.63% d.m.), lignin (0.83% d.m.), and elevated water extract viscosity (5.21 mPa·s). Hybrid cultivars were characterized by lower protein content and lower amylolytic activity, while no significant differences between hybrid and population cultivars were found in terms of dietary fiber and its components.