Flow cytometry is one of the standard methods for abundance determinations of prokaryotes, picophytoplankton and viruses in aquatic environment; it is a very popular tool based on the simplicity of the protocols and the fast processing of samples. In a regular oceanographic cruise these abundance measures are collected through a Niskin bottle following a sample plan of stations spatially divided by e.g. kilometers. Nevertheless, precisely for its simplicity and velocity, flow-cytometry is a perfect tool for continuous measurements. Here we test the use of a continuous automated sampling machine (OC-300) connected to a flow-cytometer (Accuri-C6) to estimate abundance, relative size and phenotypic diversity of prokaryotes in marine surface waters every 15 min for 5 days during a short Mediterranean cruise. Sea-water was taken by a faucet linked to a continuum pump (5 m depth). Once taken the sample, the Oncyt-300 stains it and sends it to the flow-cytometer. Through this method we achieved a fine-grain scale view of microbial community composition both during space and during time. It is worth to highlight that it was also possible to keep measuring during a storm, a common event during a cruise, taking advantage of the entire duration of the cruise. The measured features (abundance and size) were associated with metadata (temperature, salinity, conductivity, etc) also taken in continuous and used to study the effect of the environment on microbial community structure. The dataset produced (which included the optical properties of every single cell measured) it is also perfectly tailored for application of cytometric fingerprinting which is used to understand how phenotypic diversity, based on populations with common optical properties, varies along space and time. The OC-300 has previously been used in bioreactors and culture experiment but this is the first time it is applied to the marine environment directly in MIAU oceanographic cruise. Due to its high-resolution, we foresee great potentiality to this application both, to cover large sampling areas and to in situ monitor day-night cycles.