Nowadays, hydropower plays an essential role in the energy market. Due to their fast response and regulation capacity, hydraulic turbines operate at off-design conditions with a high number of starts and stops. In this situation, dynamic loads and stresses over the structure are high, registering some failures over time, especially in the runner. Therefore, it is important to know the dynamic response of the runner while in operation, i.e., the natural frequencies, damping and mode shapes, in order to avoid resonance and fatigue problems. Detecting the natural frequencies of hydraulic turbine runners while in operation is challenging, because they are inaccessible structures strongly affected by their confinement in water. Strain gauges are used to measure the stresses of hydraulic turbine runners in operation during commissioning. However, in this paper, the feasibility of using them to detect the natural frequencies of hydraulic turbines runners while in operation is studied. For this purpose, a large Francis turbine runner (444 MW) was instrumented with several strain gauges at different positions. First, a complete experimental strain modal testing (SMT) of the runner in air was performed using the strain gauges and accelerometers. Then, the natural frequencies of the runner were estimated during operation by means of analyzing accurately transient events or rough operating conditions.