It is crucial to understand and predict how the water and sediment flow in mountain channels for better disaster risk management. Detailed and quantitative measurement of channel and stream-bed structure is in great demand. In this paper, the utility of greenwavelength TLS for measurement of submerged stream-bed is preliminary examined in a steep mountain channel. The ability of through water measurement is evaluated in terms of water depth and flow velocity. Automated extraction of submerged objects is also tested. The results of comparison of water depth derived by TLS and survey displayed significant correlation between them, presenting good performance of green-wavelength TLS for measurement of submerged stream-bed. The analysis using a Generalized Liner Model (GLM) indicated that each of water depth and flow velocity alone does not affect the accuracy of TLS measurement, however, the interaction between water depth and flow velocity may have an influence. The attempt to automatically extract the dimension of submerged objects was partially successful, achieving maximum error of +0.8 cm for two objects.