Changes in both land use and climate can alter the balance of transport capacity and sediment supply in rivers. Hence, the primary driver of recent incision or aggradation in alluvial channels is often unclear. The San Lorenzo River on the central coast of California is one location where both climate and land use—specifically, clear-cut forestry of coastal redwoods—could explain recent vertical incision and floodplain abandonment. At our field site on the San Lorenzo, we estimate the magnitude of recent incision using both the ratio of bankfull to critical Shields numbers (𝜏^∗_𝑏𝑓/𝜏^∗_𝑐) and the geomorphically effective discharge, calculated from historical gauge data. The Shields number ratio suggests that the normalized bankfull stress of the San Lorenzo River is in the upper 1–2% of West Coast rivers, and the effective discharge corresponds to flow depths ~2–4 m below current bankfull conditions. Radiocarbon ages from detrital charcoal in floodplain sediment reveal active floodplain deposition during the 1600s and possibly into the 1800s, constraining the timing of incision to the last few centuries. Multiple hanging tributaries above the mainstem San Lorenzo River, along with patterns in vegetation on terrace surfaces, corroborate our estimates of the magnitude and timing of incision. Taken together, our findings suggest that floodplain abandonment in this reach was mainly due to methods employed during logging that increased shear stress on the channel bed and reduced sediment storage capacity. We suggest that direct channel modifications in rivers can counterbalance increases in sediment delivery due to clear-cutting, resulting in channel incision rather than aggradation. Today, a young, lower surface appears to be forming adjacent to the San Lorenzo River, which we interpret as an incipient floodplain that is in equilibrium with modern sediment supply and transport capacity.