The distributions of aquatic macrophytes were examined in relation to the chemical structure of pool-riffle-pool hyporheic zones in a northern Michigan river. Submersed Potamogeton filiformis, P. richardsonii, Veronica catenata, and Chara vulgaris, which are assumed to take in nutrients primarily through the root systems, were associated with hyporheic upwelling at the downstream end of riffles that often contain high amounts of ammonium (NH4). Potamogeton gramineus, which relies more on stream water as the primary nutrient source, was associated more with hyporheic downwelling areas. Emergent Sparganium chlorocarpum and Sagittaria latifolia were most abundant in reduced currents at the margins of riffles which also were potentially richer in soluble reactive phosphorus (SRP) and NH4 than surface water. Where the physical conditions of light, surface flow, sediment structure, etc. are met, subsurface flow patterns and the resulting chemical composition of interstitial waters may be the most important factors in establishing habitats and maintaining productivity in aquatic macrophytes.