The Rhone River provides the largest inputs of terrestrial freshwater and nutrients into the Mediterranean Sea. The Rhone River diluted water intrusions into the Bay of Marseille were investigated, examining their physical generation processes and associated biogeochemical impact by using in situ observations, remote sensing data, and a three-dimensional physical/biogeochemical coupled model. During our study period from 2007 to 2011, Rhone River intrusions occurred on average 7.6 times per year and affected more frequently the northern part of the bay. A classification of intrusion events in three categories is proposed (short lived, big, and small) as a function of their duration and spatial extent. The intrusions appeared to be driven by: (i) wind forcing, (ii) the presence of a mesoscale eddy, (iii) the Rhone River discharge volume, and (iv) the variation in thermocline depth. Typically, a combination of these favorable factors was necessary to induce an intrusion. An intrusion strongly impacts the biogeochemical functioning of the Bay of Marseille by bringing large quantities of nutrients into the bay. Mass balances were computed allowing us to quantify this impact on the Bay of Marseille. The results show that the ecological impact depends very much on the type of intrusion, with big intrusions having the highest impact.