Groundwater which occurs in fractured rock or porous aquifers or other geological weak zones such as faults and fractures is usually extracted via boreholes, hand wells or other sources such as springs. Water scarcity has become a severe problem due to many factors, such as an alarming increase in population and per capita water consumption, over exploitation of groundwater resources and abrupt global climatic change along with its related eco-environmental geological problems. In such situation, application of artificial recharge systems (e.g. surface recharge basin and deep injection well systems) can help to effectively manage and augment the unitization of groundwater resources. However, the clogging problem, which may be caused by a complex interdependent mechanisms of physical, chemical and biological has been a challenge for the efficacy and the implementation of recharge facilities. Clogging can reduce the permeability, recharge rate and longevity of recharge facilities and increase the operational and maintenance costs. Major influencing factors associated with the occurrence of clogging include the chemical composition of groundwater (both the recharge water and native groundwater), aquifer medium and microbial diversity, together with other environmental factors such as temperature, pressure, total dissolved solids, total soluble salts, pH, Eh, nutrients, gases, carbonates and others; these factors ultimately increase the piezometric head but reduce the permeability and infiltration rates of porous/seepage media. Pretreatment of recharge water can minimize the potential clogging. In the case of clogged wells, rehabilitation methods need to be deployed. In the meantime, there is an urgent needs to understand the basic causes and developmental processes/mechanisms of clogging in order to mitigate this problem. This paper reviews the major clogging mechanisms and their possible preventive measures and redevelopments in artificial recharge systems.