Relatively little is known about the role of perched aquifers in hydrological, biogeochemical, and biological processes of vernal pool landscapes. The objectives of this study are to introduce a perched aquifer concept for vernal pool formation and maintenance and to examine the resulting hydrological and biogeochemical phenomena in a representative catchment with three vernal pools connected to one another and to a seasonal stream by swales. A combined hydrometric and geochemical approach was used. Annual rainfall infiltrated but perched on a claypan/duripan, and this perched groundwater flowed downgradient toward the seasonal stream. The upper layer of soil above the claypan/duripan is ∼0·6 m in thickness in the uplands and ∼0·1 m in thickness in the vernal pools. Some groundwater flowed through the vernal pools when heads in the perched aquifer exceeded ∼0·1 m above the claypan/duripan. Perched groundwater discharge accounted for 30–60% of the inflow to the vernal pools during and immediately following storm events. However, most perched groundwater flowed under or around the vernal pools or was recharged by annual rainfall downgradient of the vernal pools. Most of the perched groundwater was discharged to the outlet swale immediately upgradient of the seasonal stream, and most water discharging from the outlet swale to the seasonal stream was perched groundwater that had not flowed through the vernal pools. Therefore, nitrate‐nitrogen concentrations were lower (e.g. 0·17 to 0·39 mg l−1) and dissolved organic carbon concentrations were higher (e.g. 5·97 to 3·24 mg l−1) in vernal pool water than in outlet swale water discharging to the seasonal stream. Though the uplands, vernal pools, and seasonal stream are part of a single surface‐water and perched groundwater system, the vernal pools apparently play a limited role in controlling landscape‐scale water quality. Copyright © 2005 John Wiley & Sons, Ltd.