Potamogeton praelongus is a perennial aquatic plant with a long perennial rhizome. Shoot length varies from several tens of centimeters to several meters depending on water depth and transparency, which affects the amount of available solar radiation. The shoot length of plants growing in the Czech Republic varies from 30 to 150 cm, while in Scandinavian lakes the stems can be more than 300 cm long. The shoot is round, simple or branched, with a zig-zag turningat the nodes. Submerged leaves are 50–180 mm long, 14–40 mm wide, 3.5–12.0 times longer than wide, slightly transparent, fresh to dark green, lanceolate, and sessile. The leaf base is semi-round, the tip is obtuse or cowled, the leaf edge is entire non-toothed, and the leaves have 11–23 veins. Emerged leaves are not developed. Stipules are from whitish to pale green, 10–80 mm long, and grown together on the leaf side. Length of the inflorescence is 25–55 mm, and its peduncles are 60–200 mm long. In favourable ecologic conditions, it blooms from May to July and the spikes rise above the surface for a short time. Then they descend into the water and produce achenes. The spike peduncles gradually rot off and the achenes sink to the bottom. Achenes are dark green, 4.2–5.8 mm long, elliptic with a sharp dorsal keel and hard pericarp which gets darker with time. The embryo is coiled inside the seed.
The taxon can be mistaken for red pondweed (Potamogeton alpinus), which however creates emerged leaves. These are often reddish and turn red or ferruginous when drying out. Red pondweed has a straight shoot, stipules are ochre-white or rusty brown. The high morphologic variability of this taxon is similar to that of other aquatic plants and is caused by phenotypic plasticity induced by the variability of the water environment. Morphologic variability is most apparent in shoot length and branching, leaf shape and size, length of internodes, and length of inflorescence peduncles.