The ecosystem health of the Toronto Waterfront (Ashbridges Bay), Lake Ontario which receives treated sewage effluent was investigated during 1987 and 1988 by means of a functional and structural battery of tests. The functional tests included in situ size-fractionated primary productivity, Algal Fractionation Bioassays (AFBs), unfiltered and filtered bioassays, and sediment assays with Daphnia magna and Hyalella azteca. The structural evaluation involved the biomonitoring of the components of the ‘microbial loop’, such as bacteria, autotrophic picoplankton, heterotrophic nanoflagellates, and protozoa. The experimental results reveal a diversity of physiological responses to the complex nutrient and contaminant regimes by the indigenous phytoplankton. There was no evidence of the impact of chlorination on the primary productivity of the Bay. The overall productivity was higher during the post-chlorination period than the pre-chlorination phase. The high rates of microplankton + netplankton productivity near the outfall have been attributed to the bioavailability of nutrients which, quite possibly, exert ameliorating effects on metal toxicity. In contrast, the low ultraplankton rates have been interpreted to be due to their well-known sensitivity to contaminants. The Effluent Receiving Water Bioassays (ERWB) with filtered and unfiltered experiments provided interesting insight and appear to be a potentially useful assessment tool. Generally, the unfiltered water compared to the filtered was toxic to the offshore test phytoplankton. This demonstrates a unique ecological adaptation to the prevailing in situ conditions by the Bay community which might be important from the restoration point of view. However, the offshore population was found to be sensitive to the particulate-bound toxicity as indicated by the unfiltered bioassays. Consequently, it is essential to probe the complexity of nutrient-contaminant interactions which ultimately appear to determine the toxicity and the resulting health of the biota. Furthermore, our experiments have shown that the particulate-matter is an important carrier of both nutrients and contaminants in Ashbridges Bay. The sediment bioassays for Station 419 indicated that sediments were toxic during both the pre- and post-chlorination phases. Both solid and liquid phase testing indicated toxicity of sediment to the acute Daphnia test. The Hyalella chronic assay showed good survival during the 4-wk period of the experiment, in contrast to the toxicity observed for phytoplankton and Daphnia. This may be due to large mounts of organic matter available in the Bay. The invertebrate bioassays confirmed the lack of impact of chlorination. Finally, the ‘microbial loop’ seems to be a sensitive, rapid, and an early warning bioindicator of anthropogenic stress. The multi-trophic battery of structural and functional strategy adopted in our laboratory appear to be holistic and effective. The strategy has a considerable potential for developing eco-technology for a badly needed assessment and restoration of ecosystem health of the Great Lakes as well as other perturbed environments in the world.