Symptoms of Septoria brown spot include numerous small, irregular, dark brown spots on the leaves. These spots (lesions) frequently merge to form irregularly shaped brown blotches, especially along leaf edges or leaf veins. Infected leaves turn yellow and drop prematurely.

Early stages of brown spot can be mistaken for bacterial blight. Both diseases often occur in the same fields and even the same plant, and symptoms can be difficult to separate. Typically, Septoria brown spot infection begins on oldest leaves, whereas bacterial blight occurs on the newest leaves. In the earliest stages of disease development, bacterial leaf blight lesions usually have a yellow halo around each lesion. With brown spot, entire leaves will turn yellow and drop from the plant, whereas bacterial leaf blight infected leaves remain attached. As bacterial blight continues to develop, the lesions will coalesce and the diseased tissue will fall out, giving the leaf a tattered appearance.