Vassova lagoon is a typical Mediterranean (small, shallow, micro-tidal, well-mixed) coastal lagoon, receiving limited seasonal freshwater inflows from direct precipitation and underground seepage. An intensive study was carried out in order to quantify the mechanisms responsible for the intra-tidal and residual transport of water, salt, nutrients and chlorophyll at the mouth of this lagoon and to assess the lagoon's flushing behavior. Results indicated that although the system is micro-tidal, tidal effects appeared to be the dominant factor for the longitudinal distribution of physical and chemical parameters, while the associated residual flow is also important and serves as a baseline measure of overall circulation. However, analysis of the net longitudinal currents and fluxes of water, salt and nutrients revealed the importance of non-tidal effects (wind effect and precipitation incidents) in the mean tidal transport. It is shown that the Eulerian residual currents transported water and its properties inwards under southern winds, while a seaward transport was induced during precipitation incidents and northern winds. The Stokes drift effect was found an order of magnitude lower than the Eulerian current, directed towards the lagoon, proving the partially-progressive nature of the tide. Nutrients and chlorophyll-alpha loads are exported from the lagoon to the open sea during the ebb phase of the autumn and winter tidal cycles, associated with the inflow of nutrient-rich freshwater, seeped through the surrounding drainage canal. The reverse transport occurs in spring and early summer, when nutrients enter the lagoon during the flood tidal phase, from the nutrient-rich upper layer of the stratified adjacent sea. Application of a tidal prism model shows that Vassova lagoon has a mean flushing time of 7.5 days, ranging between 4 to 18 days, affected inversely by the tidal oscillation.