Heat oil in a skillet over medium heat. Add onions; cook and stir until fragrant, about 1 minute. Toss in fava beans and cook until slightly tender, about 2 minutes.
Mix 2 tablespoons water and flour together in a bowl; pour into the fava bean mixture. Add 1 cup water, lemon juice, sugar, and salt. Cover and bring to a boil. Reduce heat to low and simmer until fava beans are very tender, about 5 minutes.
Stir dill into the fava bean mixture; continue simmering until flavors are combined, about 2 minutes. Let cool to room temperature.