Abstract Seasonal variations in the primary production regime in the upper water column were assessed by shipboard observations using hydrocasts and natural fluorescence profiling at a fixed station in the central part of Sagami Bay, Japan. The observations were conducted as a part of ‘Project Sagami’ dedicated to the interdisciplinary study of seasonality in bathyal benthic populations and its coupling with water column processes. Based on the time-series observations at intervals of about 1 to 2 months, primary productivity in terms of chlorophyll abundance appeared to be elevated during the spring of 1997, but the observed peaks of biomass were much less significant in the spring of 1998. Meanwhile, the organic matter flux, as indicated by sediment trap data and benthic observations, had a significant peak in the spring of 1998 as well, and its magnitude was comparable to that in 1997. Satellite images of ocean color obtained during the spring of 1997 indicate the importance of events with time scales much shorter than a month, and suggest qualitative differences in the phytoplankton community in the euphotic zone for each bloom event during this period. The possible mechanisms that could yield the spring maximum of material input to the benthic community are discussed.