The particular structure and configuration of the Venice lagoon represents a paramount case study concerning coastal flooding which affects natural, historical/cultural properties, together with industrial, commercial, economical and port activities. In order to defend Venice (and other sites) within the lagoon from severe floods, the Italian Government promoted the construction of a complex hydraulic/maritime system, including a movable storm surge barrier named Experimental Electromechanical Module (MoSE), to be activated when specific water levels occur. When the MoSE barriers are raised, the only access to the lagoon for commercial and cruise ships is represented by the Malamocco lock gate, provided that suitable safety conditions (involving the significant wave height) are satisfied. In addition, the Italian Government has recently established that, in the near future, large ships will always have to enter/exit the lagoon only through the Malamocco gate. In turn, the navigation within the Venice lagoon is (will be) controlled by the combined MoSE-Malamocco system, ruled by both univariate and bivariate paradigms/guidelines. As a novelty, in the present work, for the first time, the statistics of significant wave heights and water levels in the Venice lagoon (both univariate and bivariate ones) are investigated: in particular, these variables turn out to be dependent, and their joint occurrence (statistically modeled via Copulas) can determine the stop of ship navigation, yielding significant economic losses. Here, univariate and bivariate Return Periods and Failure Probabilities are used to thoroughly model the statistical behavior of significant wave heights and water levels, in order to provide useful quantitative indications for the management of the tricky hydraulic, maritime and economical system of the Venice lagoon.