Aquifer artificial recharge from surface infiltration ponds is often conducted to replenish depleted aquifers in arid and semi-arid zones. Physical and bio-geochemical clogging decreases the host soil’s infiltration capacity, which has to be restored with periodic maintenance activities. We develop a probabilistic modeling framework that quantifies the risk of a pond’s infiltration capacity falling below its target value due to soil heterogeneity and clogging. This framework can act as a tool to aid managers in optimally selecting and designing maintenance strategies. Our model enables one to account for a variety of maintenance strategies that target different clogging mechanisms. The framework is applied to an existing pond in Barcelona, Spain as well as to several synthetic infiltration ponds with varying statistical distributions of initial infiltration capacity. We find that physical clogging mechanisms induce the greatest uncertainty and that maintenance targeted at these can yield optimal results. However, considering the fundamental role of the spatial variability in the initial properties, we conclude that an adequate initial characterization of the surface infiltration ponds is crucial to determining the degree of uncertainty of different maintenance solutions and thus to making cost-effective and reliable decisions.