Additional storage of water is a potential option to meet future water supply goals. Financial comparisons are needed to improve decision making about whether to store water in surface reservoirs or below ground, using managed aquifer recharge (MAR). In some places, the results of cost-benefit analysis show that MAR is financially superior to surface storage. However, uncertainty often exists as to whether MAR systems will remain operationally effective and profitable in the future, because the profitability of MAR is dependent on many uncertain technical and financial variables. This paper introduces a method to assess the financial feasibility of MAR under uncertainty. We assess such uncertainties by identification of cross-over points in break-even analysis. Cross-over points are the thresholds where MAR and surface storage have equal financial returns. Such thresholds can be interpreted as a set of minimum requirements beyond which an investment in MAR may no longer be worthwhile. Checking that these thresholds are satisfied can improve confidence in decision making. Our suggested approach can also be used to identify areas that may not be suitable for MAR, thereby avoiding expensive hydrogeological and geophysical investigations.