Submerged water plants can be divided into two main types. Underwater plants that grow with their foliage totally submerged underwater, such as Eel grass (Vallisneria). Emergent water plants with foliage both under the water and also on or above the water surface, such as Water Milfoil (Myriophyllum species).

In general, a favorable ratio of surface (high) with respect to volume (small) is encountered. Fresh water plants have no water balance problems. They exchange gas optimally without risk of dessication through the thin cuticle which is air-permeable; the epidermis is also thin or event absent. Seagrasses by contrast have to struggle against the high salinity in their environment. The external cell wall is not so thin as in fresh water plants. The vascular system in water plants is reduced in general. Their buoyancy derives from large intercellular cavities that protrude into stems and roots and thus facilitate oxygen transport (Microscopical fluorescence and bright field views of aerenchym in a Zostera leaf). The intensity of light underwater is relatively low; a true palisade parenchyma layer is often lacking.

Submerged plants have stems and leaves that grow entirely underwater, although some may also have floating leaves. Flowers and seeds on short stems that extend above the water may also be present. Submerged plants grow from near shore to the deepest part of the littoral zone and display a wide range of plant shapes. Depending on the species, they may form a low-growing "meadow" near the lake bottom, grow with lots of open space between plant stems, or form dense stands or surface mats.