During early tree development, it is important to remove suckers from the base of the tree. These are likely to be from the rootstock and will not produce desirable fruit. Also, they may eventually interfere with proper tree development.

Mature citrus do not need canopy pruning for health or production except when injury has occurred from freezes, disease, etc. However, pruning may sometimes be necessary to prevent crowding other plants, structures, or reserved open spaces. When pruning, remove only the minimum amount of canopy necessary since reduction of harvest will be greatest with severe canopy removal.

Trees sometimes produce vigorous vertical shoots within the canopy that are known as water shoots. Since they are slow to bear and often interfere with more productive branches, their removal is recommended. When pruning, do not leave branch stubs which could be attacked by fungus and potentially damage the tree. Rather, make the cut just beyond the “collar” of the branch or limb to be removed. 

Additional Resource 

http://edis.ifas.ufl.edu/HS121