Agricultural intensification has led to dramatic losses in biodiversity over the past several decades. Many studies have shown the effects of intensification on vegetation or soil communities at field or local scales. However, the functional significance of biodiversity may only appear at larger spatial and temporal scales, due to exchanges among local ecosystems throughout a landscape. To examine how patterns of biodiversity loss are reflected at larger spatial scales, plant and soil biodiversity and associated indicators of ecosystem functions were assessed in riparian areas over a 150 km2 agricultural landscape in the Sacramento Valley of California. Publicly-available GIS data were first used to classify and select sites over the range of soils, topography and plant community types. Representative sites from the landscape were sampled for soil physiochemical properties, as well as microbial, nematode, and plant communities. Higher agricultural intensification, based on field and landscape indices, was negatively correlated with richness and diversity of plant and soil taxa, and was related to indicators of ecosystem functions, such as increased soil nitrate and phosphorus loading, decreased riparian health ratings, and lower soil carbon, soil microbial biomass and soil food web structure. Both field- and landscape-scale factors played important roles in the measured losses. The study area was composed of a wide array of soils, vegetation, and land management, indicating that the observed trends transcended site-specific conditions. © 2010 Springer Science+Business Media B.V.