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This collection provides a multi-year time series of water quality parameters, including nutrient levels, phytoplankton triggers, and seagrass coverage, specifically for the Swan Canning Estuary in Western Australia. It supports longitudinal analysis of ecosystem health, compliance with water quality targets, and the modeling of system responses to environmental changes and management actions. The data originates from official government monitoring programs, offering a consistent and authoritative record for researchers and resource managers focused on this critical estuarine system.