Understanding the interactions between belowground and aboveground process and how they respond to annual climatic variability remains a challenging task. In this study, we combined molecular techniques with high frequency images from automated minirhizotrons to determine the identity and temporal variability of fine roots and mycorrhizal fungi in a mixed-conifer forest in Southern California. We also examined how changes in fine roots and mycorrhizal fungi are related to leaf phenology and water dynamics over the course of the growing season. Throughout the study, there was considerable variation in ectomycorrhizal roots, with greater ectomycorrhizal roots during the dry summer months compared to early spring. Although the total number of ectomycorrhizal fungi did not change, there was a significant change in the ectomycorrhizal fungal community over the course of the growing season. Arbuscular mycorrhizal roots, on the other hand, showed little variation during the growing season. Sap flow peaked in mid-June, and corresponded well to the formation of new leaves and a period of relatively high soil moisture. Soil respiration varied between 1 µmol CO2 m-2 s-1 and 3.5 µmol CO2 m-2 s-1 during the year, with greater rates corresponding to periods of relatively high soil moisture and high soil temperature. By integrating data from a wide range of sensors, we can better understand the biophysical factors influencing the flux of carbon and water through an ecosystem.