Marine waters can be highly heterogeneous both on a spatial and temporal scale, yet monitoring is currently mainly limited to low-resolution methods. This study explores the use of two high-resolution methods to study phytoplankton dynamics; Fast Repetition Rate fluorometry (FRRf) to study phytoplankton photosynthesis and scanning flowcytometry (FCM) to study phytoplankton biomass and composition. Measurements were conducted during four cruises on the Dutch North Sea in April, May, June, and August of 2017. Both FRRf and FCM data show spatial heterogeneity with monthly variation. Automated unsupervised Hidden Markov Model (uHMM) spatial clustering resulted in the identification of regions with distinct phytoplankton communities. Manual adjustments were necessary to optimize visualization of some distinct phytoplankton communities. Stepwise multiple linear regression (n = 61) revealed that photophysiology (alpha), phytoplankton biomass (total red fluorescence) and abiotic predictors (Turbidity, DIN, time of the day and temperature) determined integrated water column gross primary productivity. Apart from spatial heterogeneity, the diurnal trend is a significant predictor exposing clear trends with other photophysiological parameters. Consequently, spatial patterns are difficult as temporal and spatial patterns occur simultaneously. Nevertheless, high-resolution monitoring is a very useful supplement in addition to regular low-resolution monitoring.