Citrus trees can be pruned, but they do not require extensive pruning to produce fruit. Any shoots, known as “suckers”, which grow from below the graft union should be removed whenever they appear. The best time to prune citrus trees is in late winter or early spring after the danger of frost has passed. Dead, diseased or broken branches can be removed at any time. Young trees should be pruned as little as possible since the removal of leaves slows their growth. Pruning of mature trees may include thinning out unwanted growth and shortening or removing low branches to keep them from touching the ground.
Vigorous upright shoots called “water sprouts” often grow above the graft union on the trunk or branches in the tree's canopy. These shoots should be retained if they are in a good location since they increase the tree's size and its fruit bearing capacity. Shoots that grow up through the center of a tree can be pulled outward into an open area of the tree or pruned out if they are not needed. Water sprouts left unpruned usually produce lateral branching within a year, but they can be shortened if desired.
By V. Lazaneo, Urban Horticulture Advisor, Emeritus, UC Cooperative Extension, August 2012