Since 1981, water allocation in Chile has been based on a water use rights (WURs) market, with limited regulatory and supervisory mechanisms. The volume to be granted as permanent and eventual WURs is calculated from streamflow records, if stream gauge data are available, or from hydrologic parameter transfer from gauged to ungauged catchments, usually with less than 50 years of record. To test the performance of this allocation system, while analyzing the long-term natural variability in water resources, we investigated a 400 year-long (1590–2015) tree-ring reconstruction of runoff and historical water rights for Perquilauquén at Quella catchment, a tributary to the Maule River in Central Chile (35°S–36°30S). Furthermore, we assess how the current legislation would perform under a projected climate scenario, based on historical climate simulations of runoff calibrated against observed data, and future projections. Our analyses indicate that the allocation methodology currently applied by the Water Authority in Chile is very sensitive to the time window of data used, which leads to an underestimation of variability and long-term trends. According to the WURs database provided by the Chilean Water Directorate, WURs at Perquilauquén at Quella are already over-allocated. Considering regional climate projections, this condition will be exacerbated in the future. Furthermore, serious problems regarding the access and quality of information on already-granted WURs and actual water usage have been diagnosed, which further encumber environmental strategies to deal with and adapt to climate change. We emphasize the urgent need for a review and revision of current water allocation methodologies and water law in Chile, which are not concordant with the dynamics and non-stationarity of hydrological processes. Water scarcity and water governance are two of the key issues to be faced by Chile in the Anthropocene.