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The present contribution describes an electrochemical system for the detection of alkaline phosphatase (ALP) enzyme inhibitors in seawater medium. Fluorescence spectroscopy and thermal unfolding results suggest that the state of free ALP is affected in this medium, yet the protein remains active. The enzyme activity can be evaluated using hydroquinone diphosphate as the substrate, with hydroquinone as the electrochemically monitored product. It has been demonstrated that encapsulation in conventional and organic modified silica matrices maintains ALP integrity, although diffusion across the formed monoliths hinders the electrochemical response. ALP@Phenyl-modified silica exhibits the best performance due to higher affinity between substrate molecules and aromatic moieties and, probably, to larger pore size. This electrochemical system can detect and quantify calyculin A in seawater at sub-nanomolar concentrations and it can also be employed for the development of electrochemical biosensors tailored for the marine environment.