In intermittent rivers and ephemeral streams (hereafter, IRES), hydrological connectivity mediated by either flowing or nonflowing water extends along three spatial dimensions—longitudinal, lateral, and vertical—and varies over time. Flow intermittence disrupts this connectivity, operating through complex hydrological transitions (e.g., between flowing and nonflowing phases). These transitions occur concurrently and interact along all three spatial dimensions, primarily driven by flow regime and catchment geomorphology, modified by human activities. Longitudinally, streamflow cessation and drying interrupt hydrological connectivity, contributing to physicochemical patchiness, habitat isolation, and fragmentation of metapopulations and metacommunities. Laterally, hydrological connectivity established during overbank flows is lost when water levels fall, reducing water-mediated transfers of energy, materials, and organisms from the floodplain and riparian zone. Vertically, flow cessation impairs exchange of surface and shallow groundwater, severely altering hydrological, chemical, and microbial gradients within the sediments. Concurrent interactions and physical discontinuities in hydrological connectivity along these three dimensions produce complex mosaics of physicochemical patches at different scales whose boundaries fluctuate over time in response to the flow regime. This complex patchiness underpins the characteristic physical, chemical, and biological diversity at multiple scales along longitudinal, lateral, and vertical hydrological dimensions in IRES.