Dissolved organic matter (DOM) in the ocean is one of the largest carbon pools on earth, similar in size to atmospheric CO2. Due to its richness in energy and nutrients it is fundamental for marine food webs and for microbial life. The microbial loop is an essential compartment in the global carbon cycle and is important for the transformation and recycling of organic matter and nutrients in the oceans. Microbial communities shape the molecular composition of DOM and vice versa. Earlier studies have shown that seasonal dynamics in DOM composition and microbial communities exist. A central aim of the study was to explore and characterize variations in composition of bacterial communities and DOM over much shorter periods of time, ranging from hours to days. Results revealed that there was no relation between the composition of DOM and the bacterial community neither in daily sampling nor in hourly sampling. Two significantly different sample groups were distinguishable in both daily and hourly sets of samples of bacterial communities and molecular DOM composition. In contrast DOM samples taken hourly did not group significantly. Multivariate statistics (dbRDA) reveal that variations in bacterial community and DOM composition are mainly driven by salinity changes. we therfore conclude that salinity and molecules typical for marine and terrestrial organic matter are significantly correlated. Further information on bacterial community structure will be available through sequencing of bacterial DNA.