The Venice lagoon collects different realities, such as the historical Venice town, the main industries of Marghera, and a large traffic harbour. The water exchange is mainly provided by tidal movements. In such an environment, a continuous monitoring is necessary to avoid water eutrophication and pollution phenomena like sudden algal blooms and anoxia. In the framework of a national project some measurement campaigns were carried out during recent years to point out the usefulness of fluorescence lidar also in this particular marine environment. A high spectral resolution fluorescence lidar operated from different platforms along the Venice lagoon with simultaneous traditional monitoring and sampling. The experiments demonstrated the advantages of lidar remote sensing in the monitoring of the lagoon water quality. The results are comparable to conventional field measurements with the advantage that, in measurements scheduled over an extended time, the need of maintenance is not costly and tedious as for in situ measurements.