The combination of varying aquatic habitats and flow regimes creates a complex stimulus environment from which sensory information can be extracted. Previous studies with crayfish in artificial stream settings have shown that altering the temporal and spatial structure of an odor plume modifies orientation behavior. Exposure to more temporally complex odor signals enables crayfish to locate food more efficiently. To link these studies to a more natural setting, we examined how odor signals are dispersed in 3 physically different habitats within the Maple River in Pellston, Michigan, USA, by simultaneously measuring flow patterns and odor plume characteristics. These microhabitats consisted of sections of the stream with gravel, transition (gravel and sand), or sand substrate. Flow measurements were taken using an Acoustic Doppler Velocimeter while simultaneous in situ odor plume measurements were made with an Epsilon electrochemical system. Flow had more turbulent energy in gravel and transition habitats than in sand habitat. Mean velocity was significantly higher in gravel (67.8 ± 2.00 cm/s) than in transition (30.5 ± 0.46 cm/s) and sand (30.6 ± 0.27 cm/s) habitats. In addition, eddy diffusivity rates were higher in gravel (173.3 cm²/s³) than in sand (9.74 cm²/s³) and transition (129.7 cm²/s³) habitats. Differences in turbulent flow profoundly affected the fine-scale distribution of the chemical signal. The concentration of dopamine tracer in odor pulses was significantly lower in sand (range: 8.1–6.9 µmol/L) and transition (range: 26.2–8.9 µmol/L) habitats than in gravel (range: 46.5–5.39 µmol/L) habitat. Background (natural) concentrations of dopamine are undetectable with our current technology. Furthermore, spectral density of odor pulses showed larger fluctuations in chemical concentration at all frequencies (0.1–10 Hz) in gravel habitat than in sand or transition habitats. Our results illustrate the dynamic nature of turbulence structure within natural stream systems and its influence on the distribution of chemical odor signals. Our results provide evidence that natural stream settings influence both the distribution and concentration of chemical odors available for ecological and behavioral interactions. The combination of turbulence and odor plume variation creates habitat-specific information that influences orientation behavior of organisms within a river.