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.

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.