It is a herbaceous rhizomatous perennial plant growing to 90 centimetres (35 in) tall. The stems are square in cross section, green or purple, and variably hairy to almost hairless. The rhizomes are wide-spreading, fleshy, and bear fibrous roots. The leaves are ovate to ovate-lanceolate, 2 to 6 centimetres (0.79 to 2.4 in) long and 1 to 4 centimetres (0.39 to 1.6 in) broad, green (sometimes purplish), opposite, toothed, and vary from hairy to nearly hairless. The flowers are tiny, densely crowded, purple, tubular, pinkish to lilac in colour; flowering is from mid to late summer. Water Mint is pollinated by insects, and also spreads by underground rhizomes, like other species of mint. All parts of the plant have a distinctly minty smell.
As the name suggests, Water Mint occurs in the shallow margins and channels of streams, rivers, pools, dikes, ditches, canals, wet meadows, marshes and fens. If the plant grows in the water itself, it rises above the surface of the water. It generally occurs on mildly acid to calcareous (it is common on soft limestone) mineral or peaty soils. M. aquatica can occur in certain fen-meadow habitats.