Northward flowing rivers are the most vulnerable system to a general early warming trend in terms of flood risk. In a changing climate, how well we understand the variability of precipitation and streamflow and the correspondence between them determines the appropriateness and efficiency of river engineering activities, flood control structures, and water resource management policies. Using both time and frequency domain approaches, this study investigated variations and periodicities in precipitation and discharge of two neighboring northward flowing river basins, the Red River of the North (referred to hereafter as the Red River) basin and the Little Missouri River basin in North America. Additionally, this study also characterized whether the most dominant quasiperiodic climate variation El Niño Southern Oscillation (ENSO) affected regional precipitation and streamflow. Results indicated that the southern and central Red River basin experienced significant increases in precipitation and discharge, particularly in cold season, while the Little Missouri River basin had no statistically significant change in precipitation or discharge. The global atmospheric oscillation ENSO had little effects on the regional precipitation and streamflow increases in the Red River basin. Furthermore, strong spectral coherences and prominent annual/semi‐annual periodicities in precipitation and discharge were revealed, confirming how precipitation determines frequency peaks and primary oscillation cycles of discharges in both basins. By removing broad‐scale climatic driver, this study indicated that some local forcing is most likely responsible for the excessive water abundances in the Red River basin, among which agriculture land usages stand out to be the most promising driver.