The Kaipara Moana is one of the largest estuaries of the southern hemisphere and like drowned river valleys worldwide, the Kaipara’s ecosystem services are degrading. Land-based inputs are one of the major stressors to the Kaipara Moana, increasing sedimentation rates and nutrient inputs resulting in a flow-on impacts to biodiversity, etc. Policy makers and stakeholders in New Zealand have been initiating change to reduce land-runoff. However, little is known about the effectiveness of these mitigation measures on estuarine water quality. A better understanding of the underlying biochemical and physical process within estuaries is needed. This research will determine how terrestrial nutrient and sediment concentrations change along the estuarine fresh-saltwater continuum and the time-scale dependency of the underlying processes. This research will also explore the feasibility of using plankton as a novel water quality indicator. Water quality data were collected along transects in the Ōruawharo and Hōteo river mouths. The data includes; nutrient, plankton and sediment samples, turbidity and chlorophyll concentrations, and flow measurements. We present the results of the first (summer) sampling round. This research will shed a light on what’s happening in Kaipara’s muddy waters before it reaches the ocean blue. A stepping stone to efficient land-runoff management.