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Abstract Hydrologic connectivity refers to the processes and thresholds leading to water transport across a landscape. In dryland ecosystems, runoff production is mediated by the arrangement of vegetation and bare soil patches on hillslopes and the properties of ephemeral channels. In this study, we used runoff measurements at multiple scales in a small (4.67 ha) mixed shrubland catchment of the Chihuahuan Desert to identify controls on and thresholds of hillslope‐channel connectivity. By relating short‐ and long‐term hydrologic records, we also addressed whether observed changes in outlet discharge since 1977 were linked to modifications in hydrologic connectivity. Hillslope runoff production was controlled by the maximum rainfall intensity occurring in a 30‐min interval (I₃₀), with small‐to‐negligible effects of antecedent surface soil moisture, vegetation cover, or slope aspect. AnI₃₀threshold of nearly 10 mm/h activated runoff propagation from the shrubland hillslopes and through the main ephemeral channel, whereas anI₃₀threshold of about 16 mm/h was required for discharge from the catchment outlet. Since storms rarely exceedI₃₀, full hillslope‐channel connectivity occurs infrequently in the mixed shrubland, leading to <2% of the annual precipitation being converted into outlet discharge. Progressive decreases in outlet discharge since 1977 could not be explained by variations in precipitation metrics, includingI₃₀, or the process of woody plant encroachment. Instead, channel modifications from the buildup of sediment behind measurement flumes may have increased transmission losses and reduced outlet discharge. Thus, alterations in channel properties can play an important role in the long‐term (45‐year) variations of rainfall–runoff dynamics of small desert catchments.