Marine microorganisms are fundamental for life on Earth. For example, they have produced most of the oxygen existing in our planet and are essential in biogeochemical cycles and energy flow to different trophic levels. One of the critical aspects of microbial ecology is the distribution of microorganisms at spatial and temporal scales since it allows us to understand the effect of environmental factors on the structure of microbial communities. In this thesis, the aim was to determine the structure of microbial communities at three spatial scales: In the first chapter, a study was conducted on the spatiotemporal dynamics of bacterioplankton communities in a tropical estuary strongly impacted by the discharge of the Tempisque River during the rainy season. The results show high spatial heterogeneity in the communities, and represent the first report on the spatial and temporal patterns in which the bacterioplankton of the Gulf of Nicoya is structured. The second chapter determined the effect of environmental gradients on the horizontal distribution of bacterioplankton in the northwestern Mediterranean. The samples were taken along cross-shore transects so that the gradients would presumably be due to the change in environmental parameters along the transect and a dilution of the anthropogenic and terrestrial effect. Community structure was observed to vary depending on the sites, but a large fraction of the microorganisms were shared in all sampled areas, reflecting a relatively high connectivity of the communities. The third chapter presents the vertical distribution of prokaryotic and eukaryotic microorganisms within the Deep Chlorophyll Maxima (DCM) in the NW Mediterranean sea, as determined by high-resolution sampling and separating two microbial size fractions (0.2-3 and 2-20 μm). The results show that the DCM acts as a transition zone (ecotone), but despite the drastic changes observed in the relative abundance of taxa in this layer both prokaryotic and eukaryotic communities below the DCM were dominated (~70% of the sequences) by taxa already detected at the ocean surface.