The availability of water in Chile has shown signs of decline in recent decades. This is problematic because Chile’s economy depends on mining, forestry, and agricultural activities, all limited by the availability of water resources. In this study, daily, monthly and annual flows in 31 basins located in the arid–semiarid zones (29°12′ S–33°58′ S) and in the humid–subhumid zones (34°43′ S–38°30′ S) of Chile were evaluated using the Mann–Kendall trend test and the quantile–Kendall procedure during three periods: 1984–2021 (31 stations), 1975–2021 (20 stations), and 1969–2021 (18 stations). Results showed that, at the annual level, trends were predominantly negative in both climatic zones and over the three periods analyzed. In the arid–semiarid zone, a higher frequency of annual significant negative trends was found in maximum flows in 1969–2021 and 1975–2021, compared to the last period under study. The humid–subhumid zone showed significant annual negative trends in all series analyzed. At the monthly level, on the other hand, the arid-semiarid zone showed a decrease in significant negative trends as the number of years analyzed increased, for all flow types. The humid–subhumid zone did not indicate a similar defined pattern. Likewise, the quantile–Kendall procedure showed a reduction in the significant trends as the length of the time series was increased in the arid-semiarid zone, but no such pattern was observed in the humid–subhumid zone. Furthermore, a relationship was observed for the PDO and the summer month flows for both zones. Consequently, it is concluded that the flow trends are generally negative, and their statistical significance depends on the period studied.