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Current evidence suggests that integrating diverse warning systems at different biological levels may not only increase the probability of detecting threats but also mitigate their impact. Here, we propose the use of both molecular and morphological descriptors at different biological levels in sessile bivalves (a suitable biological model in monitoring programs) to collect information on the ecosystem health of coastal marine habitats. In this context, studies may be implemented on biomarkers to exploit some population features, with the aim to propose an actual monitoring program that predictively would provide possible scenarios on the species fitness and ecosystem changes. Thus, the use of quality biotic elements may provide an objective environmental monitoring method and facilitate the development of sanitary, economic, and social strategies related to sustainable exploitation.