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For 100 years, California’s State Water Resources Control Board and its predecessors have been responsible for allocating available water supplies to beneficial uses, but inaccurate and incomplete accounting of water rights has made the state ill-equipped to satisfy growing societal demands for water supply reliability and healthy ecosystems. Here, we present the first comprehensive evaluation of appropriative water rights to identify where, and to what extent, water has been dedicated to human uses relative to natural supplies. The results show that water right allocations total 400 billion cubic meters, approximately five times the state’s mean annual runoff. In the state’s major river basins, water rights account for up to 1000% of natural surface water supplies, with the greatest degree of appropriation observed in tributaries to the Sacramento and San Joaquin Rivers and in coastal streams in southern California. Comparisons with water supplies and estimates of actual use indicate substantial uncertainty in how water rights are exercised. In arid regions such as California, over-allocation of surface water coupled with trends of decreasing supply suggest that new water demands will be met by re-allocation from existing uses. Without improvements to the water rights system, growing human and environmental demands portend an intensification of regional water scarcity and social conflict. California’s legal framework for managing its water resources is largely compatible with needed reforms, but additional public investment is required to enhance the capacity of the state’s water management institutions to effectively track and regulate water rights.