Hydraulic turbines sometimes exhibit a sharp efficiency drop around the best efficiency point. The drop is known to originate from large flow separations in their draft tubes, limiting their ability to recover part of the residual kinetic energy exiting the runner. While the conditions leading to the onset of these separations are not yet understood, the potentially unstable vorticity distribution at the runner exit led to the hypothesis that those separations are the result of an interaction between the flow at the center of the draft tube and the boundary layer at the walls. To study this hypothesis, the turbulent flow inside the draft tube of a bulb turbine was measured with time-resolved particle-image velocimetry (TR-PIV). In this work, coherent structures are identified from spectral proper orthogonal decomposition (SPOD) of the velocity fields to correlate changes in their topology with the efficiency drop. Special attention is given to the periodic vortical motions in the runner's wake, whose shape and energy content are found to be linked to the flow rate. Three-dimensional reconstructions of the underlying structure reveal a shift in its topology that correlates with the efficiency drop and separations at the wall. In addition, comparisons of the SPOD coefficients with the runner position show that the phase angle between the structure and the runner remains the same for each operating condition, suggesting a link with a rotating flow imbalance in the runner blade channels.