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In the dry basins in northern Mexico, concern about rivers is focused on seasonal and long-term variations in river flows that may be attributable to climate change, since it affects the water supply for domestic, industrial, public and agricultural uses. The objective of this research was to separate daily flow components and understand the patterns in 172 time-series corresponding to five rivers in northern Mexico. The headwaters of the San Pedro, Sinaloa, Nazas-Aguanaval, San Juan and San Fernando-Soto La Marina rivers are located in the Sierra Madre Occidental and Oriental, and flow through the plains into the Pacific Ocean, the Gulf of Mexico and the Central Plateau in northern Mexico, providing over 90% of the water supply for all uses. The Rora computer program isolated the base and direct flows from the total. The Mann-Kendall test and the Seno S method evaluated the trends and magnitudes of the changes in annual and monthly flow, monthly standard deviation, and daily maximums and minimums for total, direct and base flows. The results found that the base and direct flows were in equilibrium for most of the rivers. Meanwhile, each one of the variables analyzed had statistically significant trends at 40% of the hydrometric stations. Over 26% of the stations showed a consistent reduction in flow over time. Although additional investigations are needed to quantitatively isolate the potential sources of the variations to explain the temporal trends, the causes can preliminarily be attributed to climate variability in combination with natural resource management practices. The effect of potential climate change cannot be excluded from these patterns.