Phytoplankton are the foundation of marine food webs supporting fisheries and coastal communities. They respond rapidly to physical and chemical oceanography, and changes in phytoplankton communities can impact the structure and functioning of food webs. We use a robotic microscope called an Imaging Flow Cytobot (IFCB) to continuously collect images of phytoplankton from seawater. Automated taxonomic identification of imaged phytoplankton uses a supervised machine learning approach (random forest algorithm). We deploy the IFCB on fixed (docks) and roving (aboard survey ships) platforms to autonomously monitor phytoplankton communities in aquaculture areas in Puget Sound and in the California Current System. We map the distribution and abundance of phytoplankton functional groups and their relative food value to support fisheries and aquaculture and describe their changes in relation to ocean and climate variability and change