Intermittent rivers are spatially dynamic, expanding and contracting in response to changes in water availability, but studies that explicitly examine spatial drying patterns are scarce. We used long-term data produced by citizen scientists to map wet and dry reaches of 3 different river systems to investigate mechanisms producing temporal variation in drying patterns. We quantified the total wetted river length in each survey, and calculated ecologically scaled landscape indices that indicate the carrying capacity (population size) and habitat connectivity of large and small fish metapopulations in these systems. We found that the spatial extent of perennial water decreased over the study period in 2 of the 3 study rivers: similar to 26% in the Agua Fria River from 2008 to 2016, and similar to 14% in Cienega Creek from 2006 to 2016. We also observed an similar to 8% decline in habitat connectivity for large fish in the Agua Fria River. We used multivariate structural equation models to infer causal relationships between spatial drying patterns and temperature, precipitation, streamflow, and drought conditions. These models explained 85% of year-to-year variation in the total length of wet reaches, and 63 and 55% of year-to-year variation in habitat connectivity for large and small fish, respectively. With the US Southwest shifting to an even more arid climate, our results suggest that this may reduce habitat connectivity of fish populations in this region.