The seasonal soil losses and frequent shallow landslides in the Cerrado region of Brazil have high destructive potential with social, economic, and climatic implications. As fluvial systems substantially drive such environmental threats; therefore, it is essential to conduct geological site characterization and continuously monitor the rivers' and streams' seasonal erosive potentials. However, in such unstable and sensitive conditions, traditional intrusive investigation approaches may not be safe, the geophysical investigation might offer a good alternative. For the present study, a geophysical approach (particularly the seismic method) was adopted to examine the seismic footprints and GPR site characterization of a seasonal stream in the Rua do Matto, Brasilia, Brazil. The monitoring was conducted (at a safe distance) on the intermittent stream over several durations of dry (no rain) and rainy (flood) conditions. After pre-processing the raw data, the power spectral density (PSDs) was computed as a function of several variables (wind speed), time-frequency spectrograms, ambient noise displacement root mean square (RMS), the single station horizontal-to-vertical spectral ratio (HVSR) curves. In addition, changepoint analysis was used for comparing the ambient noise with wind speed (both were well correlated). The GPR amplitude and waveform variation features were attributed to the subsurface material and the presence of boulders in the floodplain and regions (low coherence value) susceptible to erosion (weak spots). The river flows were evident in the spectrograms, HVSR curves and different patterns of RMS displacements (at selective frequency ranges). The multi-peaks that emerged on the HVSR curve are further analyzed for changes in amplitude, width and troughs possibly related to river activities and soil moisture due to rain. The approach provides the basis for non-destructive monitoring tools enabling the detection of 'seismic signatures' and weak spots of the fluvial channels for improving environmental management.