Depending on the type of substrates to which the phytobenthos is attached, they would be considered as epilithic (growing on rocks and other manmade, artificial substances), epipelic (growing on silt), episammic (growing on sand), epiphytic (growing on other plants), or epizoic (growing on animals). Epizoic phytobenthos such as Ostreobium and Symbiodinium have also been found to grow on skeletons or within corals to which they have established symbiotic relationships by exchanging nutrients.
The phytobenthos' habitats can range from freshwater systems such as rivers and lakes to coastal regions. In the marine environment, phytobenthos can be found as far back from the shore as the subtidal zones where they are consistently submerged in water. Their productivity does not extend beyond the outer boundary of the littoral zones, the region to which sunlight can still penetrate to the bottom.
With increasing depth, there is a decline in algal cover due in part to light availability. In addition to depth, turbidity can restrict the extent of light availability, which would also impact the extent of phytobenthic growth. However, phytobenthos such as Ostreobium have demonstrated capability to adapt to low-light conditions as grow in areas as deep as 200 meters. Some diatoms also demonstrated mobility and rise to the surface during the earlier part of the year.
Other physical and chemical conditions that also determine phytobenthos distributions include flow, acidity, nutrient, temperature, and the community's composition. Water flow can determine the types and distributions of phytobenthos, especially in the stream communities where the water is constantly moving. Rivers with more steady flow contribute to the stable environment that can promote the growth of phytobenthos communities.