High quality monitoring data are vital for tracking and understanding the causes of ecosystem change. We present a potentially powerful approach for phytoplankton and aquatic ecosystem monitoring, based on integration of scanning flow-cytometry for the characterization and counting of algal cells with multiparametric vertical water profiling. This approach affords high-frequency data on phytoplankton abundance, functional traits and diversity, coupled with the characterization of environmental conditions for growth over the vertical structure of a deep water body. Data from a pilot study revealed effects of an environmental disturbance event on the phytoplankton community in Lake Lugano (Switzerland), characterized by a reduction in cytometry-based functional diversity and by a period of cyanobacterial dominance. These changes were missed by traditional limnological methods, employed in parallel to high-frequency monitoring. Modeling of phytoplankton functional diversity revealed the importance of integrated spatiotemporal data, including circadian time-lags and variability over the water column, to understand the drivers of diversity and dynamic processes. The approach described represents progress toward an automated and trait-based analysis of phytoplankton natural communities. Streamlining of high-frequency measurements may represent a resource for understanding, modeling and managing aquatic ecosystems under impact of environmental change, yielding insight into processes governing phytoplankton community resistance and resilience.