The lowstand extensions of two fluvial systems from the Cascadia subduction margin are investigated using high-resolution seismic reflection data to determine the relative controls on paleodrainage morphology. We document distinct differences between the two systems, located ~40 km apart, attributed to underlying structure and lithology, shelf gradient, and drainage basin characteristics. A cross-shelf valley exists for only one of the drainage systems, the Umpqua River. The outer shelf part of the valley is a syncline, which formed a natural structural low for lowstand drainage, while the inner shelf part of the valley exhibits incision and is associated with a mid-shelf convex change is slope. The other drainage system, the Siuslaw River, did not develop an across-shelf valley and is only denoted in the seismic data by an erosional subaerial unconformity. Structural trends are perpendicular to cross-shelf drainage, supporting a more anastomosing stream morphology for the paleo-Siuslaw. The shelf edge for this system was not exposed for a long period of time during the last lowstand, preventing substantial outer shelf incision. Differences in fluvial elevation, discharge, and hinterland geology, also played a role in the cross-shelf morphologies of the paleo-Umpqua and paleo-Siuslaw. These results highlight how controls on lowstand paleodrainage morphology can change over short distances on an active margin.