This paper addresses environmental monitoring through a robust dynamic integration between biomonitor and biosensor systems, a strategy that has not been attempted before. The two systems are conceptually interrelated and methodologically correlated to a cooperative/synergistic scheme (CSS) with a view to minimise uncertainty and monitoring costs and increase reliability of pollution control and abatement. The structures and operations of the biosensor component (in terms of sensitivity, device and method versatility, nature-mimicking physicochemical mechanisms, prospects and technological input) are such that they reinforce or promote the structures and operations of the natural component (in terms of bio-surveillance, impact assessment, environmental quality indexing, stress responses, metabolic pathways, etc.) and vice versa. The bioindicator ontology presented herein, including concepts, relations and controlled vocabulary aiming at establishing an integrated methodology for mapping/assessing negative environmental externalities, provides a useful tool for the design/development/implementation of an environmental network for the monitoring of a variety of pollutants over time and space and the assessment of environmental quality; the collection of the available information and its classification into taxonomic and partonomic relations allows the construction of a database that links pollutants with organisms' response, at a phenomenological and in-depth level, considering ecological parameters, relations and geomorphologic characteristics. As a result, a computer program has been designed/developed as a decision support system and has been successfully tested on a representative population of species indigenous to southern Greece. Significantly, a novel system in the form of a rational framework at the conceptual design level has been developed, that actually contributes towards achieving a cost-effective long-term monitoring program, with the flexibility to counter on-course any (anticipated or not) variations/modifications of the surveillance environment. This novel and pioneering approach will further offer a dynamic system utilised in (a) environmental impact studies and risk assessment (positive/analytic approach), (b) decision-making in the short-run (normative/tactic approach), and (c) policy-making in the long-run (normative/strategic approach). The proposed CSS, based on the integration of multiple data sources, can establish a local area network, incorporated into/expanding to a wide area network, thus offering the potential of better predictive ability and greater lead-time warning at alarm conditions than that provided by separate, stand-alone surveillance modalities.