Phosphorous is a proximal limiting nutrient in certain oceanic regions. We studied the seasonal dynamics of inorganic and organic phosphorous utilisation over a one-year period (2012) in the NW Mediterranean. 33P-labelled bioassays and flow sorting experiments were combined to address the seasonality in turnover, concentration and uptake rates of phosphate, ATP and DNA by dominant microbial groups. In parallel, 454 pyrosequencing was conducted to link changes in phosphorus substrate utilisation to prokaryotic community composition. Although increases in organic phosphorous utilisation correspond to short phosphate turnover times, phosphate uptake also increases to the extent that the majority of community phosphorous flux is channelled through the inorganic pool, irrespective of the degree of phosphate limitation. Bacteria maintain a fairly uniform pattern phosphorous substrate utilisation throughout the year. In contrast, Synechococcus and Eukaryotic populations rely increasingly on organic phosphorous substrates during times of extreme phosphate limitation. Sequencing data is employed to elucidate whether the observed patterns in substrate utilisation correspond to metabolic flexibility of a dominant ecotype or community dynamics of Synechococcus ecotypes adapted to different phosphorous acquisition strategies.