Reduced water quality is a potential outcome from intensive finfish aquaculture. Integrated multi-trophic aquaculture (IMTA) can mitigate the negative effects of dissolved nutrients emanating from fish farms by harvesting species that extract nutrients grown at adjacent sites. In this study, a coupled 3D hydrodynamic, sediment, and biogeochemical model was used to simulate an idealized temperate test estuary. A macroalgal-based IMTA model was applied within the estuarine model, to examine the spatial pattern of phytoplankton production arising from increasing levels of finfish aquaculture and the capacity of Macrocystis pyrifera to bioremediate the impacts of nutrification. Through increasing fish farm waste loads of dissolved inorganic nitrogen (DIN), the water quality in the estuarine model was forced into a “poor water quality” classification as determined by annual mean concentration of chlorophyll. Primary production was greatest in the northern section of the estuary due to circular water motion set up by a region of freshwater influence (ROFI). A nonlinear increase in annual phytoplankton biomass was simulated (under elevated finfish loads) due to the occurrence of an additional autumn phytoplankton bloom under elevated fish farm nutrient loads. IMTA scenario results demonstrated a strong spatial variability in the capacity of M. pyrifera-based IMTA to reduce water column chlorophyll concentration. Siting macroalgae farms next to those finfish farms situated in areas of high natural phytoplankton production resulted in a “good water quality” classification for the whole system. This demonstration of the use of IMTA to improve system wide water quality is valuable for regional planners and managers as it provides an analysis and quantification of a method to achieve estuarine health and economic benefit.