Radial or mixed flow turbines are very common in industrial application, spanning turbochargers, small turbines for power generation, and energy recovery systems. Secondary flows have received a limited attention in the literature, and this papers aims to fill this gap of knowledge. The secondary flow structures in mixed flow turbines are particularly complex due to its geometry, high curvature, and the appearance of Coriolis and centrifugal forces. The focus of the present work is to investigate the evolution of secondary flows and their losses in a mixed flow turbine by using an experimentally validated three-dimensional computational fluid dynamics (CFD). The flow topology is analyzed to explain the formation and evolution of flow separations at the pressure, suction, and hub surfaces. The suction surface separation is caused by centrifugal forces, and it induces the formation of a hub separation. As the inlet velocity decreases, the hub separation increases in strength. A major feature found is the pressure surface separation, located at the leading edge tip, formed due to flow incidence; as the incidence decreases, this separation extends to the hub. Losses caused by those separations as well as the tip leakage vortex are studied by calculating locally entropy generation. Results show that the tip-leakage vortex accounts for the majority of losses (60%) and renders the losses caused by suction surface and induced hub separations to be small. The presence of the more severe hub separation was also found to have a significant detrimental effect on the turbine efficiency, which increases losses on the hub and the suction surface from 40% to 65%. Pressure surface separation, however, does not vary the total amount of losses significantly but rather redistributes the losses in the blade passage.