Analysis with a three‐dimensional variably saturated groundwater flow model provides a basic understanding of the interplay between streams and perched groundwater. A simplified, layered model of heterogeneity was used to explore these relationships. Base flow contribution from perched groundwater was evaluated with regard to varying hydrogeologic conditions, including the size and location of the fine‐sediment unit and the hydraulic conductivity of the fine‐sediment unit and surrounding coarser sediment. Simulated base flow was sustained by perched groundwater with a maximum monthly discharge in excess of 15 L/s (0.6 feet³/s) over the length of the 2000‐m stream reach. Generally, the rate of perched‐groundwater discharge to the stream was proportional to the hydraulic conductivity of sediment surrounding the stream, whereas the duration of discharge was proportional to the hydraulic conductivity of the fine‐sediment unit. Other aspects of the perched aquifer affected base flow, such as the depth of stream penetration and the size of the fine‐sediment unit. Greater stream penetration decreased the maximum base flow contribution but increased the duration of contribution. Perched groundwater provided water for riparian vegetation at the demand rate but reduced the duration of perched‐groundwater discharge nearly 75%.