Streamflows in the lowland areas of the San Juan Basin are highly variable, responding to short-duration, high-intensity thunderstorms occurring in the late spring and summer. The thunderstorms can cause floods of large magnitude, but of localized extent. Most streams of the lowlands are ephemeral or intermittent.
Streams of the high mountain areas are much less variable. Most of their flow is from snowmelt, which results in low-intensity flood peaks with long, gradual recessions. Most large mountain streams are perennial.
Small ephemeral lakes and ponds in the low-lying areas have little effect on flood flows. Larger reservoirs in the basin have varying effects on flows of rivers, ranging from complete flow control to minor regulation.
The streams of the low-lying areas are high in dissolved solids content. Sodium, bicarbonate, and sulfate are the predominant ions. The quality of the water varies during a single-flow event and season-ally. Streams in the mountains are low in dissolved solids content.
Radiochemical constituents are fairly low in most of the natural streamflow, but concentrations are higher than in streams outside of the basin.