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As part of an ongoing research program aiming at monitoring molecular changes in the tissues and metabolite trafficking in the hydrosphere of algae subjected to chemical stresses, we are discussing the various analytical techniques that have been employed to characterize, and sometimes to quantity these metabolites. High-field multinuclear and solid-state nuclear magnetic resonance (NMR) spectroscopies are powerful tools for metabolite characterization from extracts and in vivo, but quantification and kinetic aspects show some limitations. Modern MS (mass spectrometry) is extremely useful for fingerprinting samples against databases and when dealing with very low concentrations of metabolites, the limitations being set by the type of chromatographic separation and mode of detection coupled with the mass spectrometer. Regarding chemical communication, optimization in terms of resolution and efficiency of hydrosphere chemical analysis can theoretically be achieved in a system which integrates (i) a multiparametric incubation chamber, (ii) a gasphase or a liquid-phase separation system and (iii) mass spectrometer(s) equipped with one or two detectors responding to the analytical and quantitative needs. This text reviews some of the techniques that have been employed in various types of plant metabolic studies, which may serve as a basis towards an integrative analytical strategy directly applicable to the metabolomics of selected marine macrophytes.