Perched and leaky geological layers can play an important role in hydrological systems by redirecting land surface recharge and reducing total recharge volume to regional aquifers. The extent of continuity and permeability of perched layers can be key physical parameters in surface and subsurface flow connection to regional groundwater systems. A semi-permeable perched layer with discontinuities, heterogeneity, fractures and faults will inevitably increase the spatial complexity of local recharge in an otherwise simple system. Relatively little is known about how perched and leaky layers might control linkages between surface flow, shallow groundwater flow, and regional groundwater. We describe one such system in the Kawerau shallow groundwater aquifer (New Zealand), where a thin, semi-permeable and fractured layer alternates between leaky and perching behaviour. A numerical groundwater model indicates the perching layer plays a critical role in controlling the volume and spatial pattern of water exchange between surface water and local and regional groundwater systems.