Hydrologic measurements in high-grade Andean streams involve challenges for discharge estimation, caused by its torrential behavior and high flow variability. Since data collected on field are essential to describe the specific hydraulic characteristics of a stream, it is necessary to consider criteria such as the ease of implementation, economic factors and accuracy. In this study, discharge estimation were performed and compared by using the area-velocity method, and a saline dilution tracer method. This analysis allowed determining the best alternative for discharge estimation with a reduced uncertainty. The analysis was carried out in three tropical watersheds whose main streams are natural high-graded with mean depths between 0.1 and 0.5 m. To this end, 104 discharge observations were performed in control cross-sections of the Combeima, Las Perlas and Ambala rivers, part of the Combeima River and Chipalo River basins in the Colombian Andes. In the studied streams, the area-velocity method had an uncertainty of 14.35% greater than that calculated for the discharge estimations using the saline tracer, this result differ from uncertainty values reported by other authors for both approaches. This work represents a contribution to the improvement of discharge estimation for the construction of rating curves and the calibration of hydrological models, specifically in watersheds with high-grade streams.