Upwelling of nutrient rich waters along continental shelves generates highly productive marine ecosystems affectingplanktonic communities from coastal to offshore domains. Methods to constrain pelagic productivity are often based on different physiological or ecosystem processes, hence describe different biogeochemically important processes. Here, we present a multi-method process-oriented investigation of diverse productivity measures in the California Current Ecosystem (CCE) Long-Term Ecological Research study region, a complex physical environment. The data are from seven multi-day deployments over two field expeditions (spring 2016 and summer 2017) and cover a transition region from high to low productivity. Employing a Lagrangian study design, we aimed to follow the water parcels over several days, comparing 24 h in-situ measurements (C and NO, uptake, sediment trap export, dilution estimates of phytoplankton growth and microzooplankton grazing) with high-resolution productivity measurements by Fast Repetition Rate Fluorometry (FRRF) and Equilibrium Inlet Mass Spectrometry (EIMS). Our results show the importance of accounting for temporal and fine spatial scale variability when estimating ecosystem production. FRRF and EIMS measurements resolved diel patterns in gross primary and net community production. Diel productivity changes agreed well with comparable more traditional measurements. While differences in productivity metrics calculated over different time intervals were considerable, as those methods rely on different base assumptions, our data can be used to explain ecosystem processes which would otherwise have gone unnoticed. The processes resolved from this method comparison can help to further our understanding of the coupling and decoupling of surface productivity and potential carbon burial in coastal and offshore ecosystems.