The root system of most cherries are predominantly spreading and shallow, even in well-drained soils. Most roots are restricted to the upper 60 cm (24 in) of soil or less, with occasional sinker roots extending to depths of 90 to 120 cm (36 to 48 in). On wet sites, the tendency toward shallow rooting is especially pronounced. Because of this tendency to grow taller than associated species in mixed stands, cherry is vulnerable to windthrow, especially on poorly drained soils and at older ages.

The most important defoliating insects attacking cherry trees include the eastern tent caterpillar (Malacosoma americanum) and the cherry scallop shell moth (Hydria prunivorata). Infestations of these insects are sporadically heavy, with some apparent growth loss and occasional mortality if heavy defoliations occur several years in a row.

Attacks by numerous species of insects cause gum defects in cherry, resulting in reduced timber quality. Gum spots in the wood are often associated with the Agromyzid cambium miner (Phytobia pruni), the peach bark beetle (Phloeotribus liminaris), and by the lesser peachtree borer (Synathedon pictipes). A wide variety of insects can cause injury to terminal shoots of black cherry seedlings and saplings, resulting in stem deformity. Archips spp. and Contarinia cerasiserotinae are among the more important.

The most common disease is cherry leaf spot caused by Coccomyces lutescens. Large numbers of black cherry seedlings are sometimes weakened or killed by this disease. Repeated attacks reduce the vigor of larger trees. Most other foliage diseases cause little damage.

Black knot, a native disease caused by the fungus Apiosporina morbosa is common on cherry. It causes elongated rough black swellings several times the diameter of the normal stem. Small twigs may be killed within a year after infection. Large cankerous swellings, a foot or more in length, may occur on the trunks of larger trees, and where several such lesions are scattered along the bole, the tree is worthless for lumber. Cytospora leucostoma is the cause of a canker disease responsible for widespread branch mortality of black cherry in Pennsylvania. Common infection courts are decaying fruit racemes and bark fissures caused by excessive gum production following passage of the larvae of Phytobia pruni, a cambium mining insect.

Several basidiomycete fungi that cause root and butt rot of living cherry trees include Armillaria mellea, Coniophora cerebella, Polyporus berkeleyi, and Tyromyces spraguei. Many other fungi cause decay of the main trunk; these include Fomes fomentarius, Fomitopsis pinicola, Poria prunicola. P. mutans, and Laetiporus sulphureus. Damage caused by glaze storms exposes cherry trees to infection by top-rot fungi.

Porcupines girdle and kill cherry trees and also consume bark, thereby providing entry points for fungi. Meadow mice and meadow voles girdle the stem near the ground. Such damage where grass or other herbaceous cover provides suitable habitat for the mice is probably one of the major causes of planting failure in unregenerated clearcuts and old fields.
White-tailed deer, rabbits, and hare feed on black cherry seedlings. In parts of Pennsylvania, deer browsing is the most serious problem of cherry trees.

Cherry is often infested with tent caterpillars in springtime. These pests can strip a tree of foliage in a matter of days.

This tent was found on wild plum, Prunus americana. It contained about 100 caterpillars and 1 lb. frass pellets.

Cherries are an important source of mast for many nongame birds, squirrel, deer, turkey, mice and moles, and other wildlife. The leaves, twigs, and bark of black cherry contain cyanide in bound form as the cyanogenic glycoside, prunasin. During foliage wilting, cyanide is released and domestic livestock that eat wilted foliage may get sick or die. Deer eat unwilted foliage without harm.

The bark has medicinal properties. In the southern Appalachians, bark is stripped from young black cherries for use in cough medicines, tonics, and sedatives (36,39). The fruit is used for making jelly and wine. Appalachian pioneers sometimes flavored their rum or brandy with the fruit to make a drink called cherry bounce. To this, the species owes one of its names, rum cherry.