Subsurface conduit flow is a critical element of investigating groundwater movement in karst regions, and it is still poorly understood due to complexity of subsurface conduit geometries and the nonlinearity of the conduit flux-hydraulic gradient relationship. A significant nature of the flow nonlinearity is the occurrence of different eddies in conduits. To reveal the nonlinear nature of conduit flow, this study investigates the influence of the eddy effect on the hydraulic gradient of different rough conduits based on extensive high-fidelity numerical simulations. Overall, the hydraulic gradients of all types of rough conduits show quadratic relations with an increase in the specific discharge. In addition, the triangular rough conduit has the largest hydraulic gradient, which gradually decreases as the shape coefficient (which is used to quantify rough elements) increases. We have identified the development and evolution of eddies in different types of rough conduits in detail. This study shows that a larger specific discharge leads to a larger eddy area, and the hydraulic gradient changes exponentially with the eddy area ratio within a limited range. Finally, the relationships among specific discharges, eddy area ratio, and hydraulic gradients are constructed and summarized. The results of this investigation are helpful for developing realistic karst groundwater flow and transport models in which subsurface conduit plays a dominant role for conducting groundwater flux and mass transport.