Butano Creek drains 23 mi2 of the Santa Cruz Mountains, San Mateo County, CA. Land use and channel management practices in the last two centuries have doubled sediment input, disconnected channels from their floodplains through incision, eliminated floodplain sediment storage and led to flooding issues in the lower watershed. Incision and floodplain disconnection not only eliminated sediment storage in the valley but also transformed floodplain storage areas into sources substantially contributing to elevated sediment loads. Removal of large wood, channel incision, and floodplain disconnection are the primary causes of a significant reduction in the complexity and function of habitats that are home to a number of sensitive and ESA-listed species. Channel change and sediment budget analyses revealed that, historically, the lowland valley functioned as a wet meadow and included an extensive well connected floodplain that provided diverse habitats. The lowland floodplain also provided sediment storage upstream of the Pescadero estuary, which is a key nursery habitat for anadromous fish species.