We examine the likelihood of delisting the Hamilton Harbour as an Area of Concern, if the nutrient loading reductions proposed by the Remedial Action Plan are actually implemented. Our analysis suggests that the chl a criterion of 10μgL−1 is achievable, but the water quality setting process should explicitly accommodate the natural variability by allowing for a realistic percentage of violations, e.g., exceedences of less than 10–15% of the weekly samples during the stratified period should still be considered as compliance of the system. The current epilimnetic total phosphorus criterion of 17μgL−1 is probably stringent and therefore a somewhat higher value (e.g., 20μgL−1) may provide a more realistic goal. Phosphorus dynamics in the sediment–water column interface need to be revisited, as the internal nutrient loading can conceivably be a regulatory factor of the duration of the transient phase and the recovery resilience of the Harbour. We also pinpoint two critical aspects of the system dynamics that invite further investigation and will likely determine our predictive capacity to assess compliance with the chlorophyll a criterion of 10μgL−1, i.e., the nutrient recycling mediated by the microbial food web and the structural shifts towards a zooplankton community dominated by large-sized and fast-growing herbivores. The latter prospect highlights the notion that the bottom-up (i.e., nutrient loading reduction) approach historically followed in the Harbour was sufficient to bring the system in its present state, but any further improvements should be viewed in the context of a combined bottom-up and top-down (i.e., alleviation of the zooplanktivorous pressure) control.