The quality of groundwater, in particular in coastal areas, is increasingly deteriorating due to the input of nutrients (NO3-, NH4+ and PO4) from septic systems and agricultural leaching. The discharge of groundwater to coastal waters, termed submarine groundwater discharge (SGD), is now recognized as an important transport pathway of nutrients from the land to the sea. The chemical composition of SGD is not only determined by the landward sources, but also by the biogeochemical reactions that occur when groundwater travels through the subterranean estuary, the zone in a coastal aquifer where freshwater and seawater interact. The aims of this thesis are: (1) To identify and quantify the biogeochemical processes that remove or transform nutrients in subterranean estuaries. (2) To assess the impact of landward source concentrations, aquifer characteristics, groundwater flow rates and dispersive transport on nutrient transformations in coastal aquifers and on the SGD of nutrients. The methodology used throughout this study is reactive transport modeling. First, a 1D finite difference reactive transport model (RTM) is used to describe the biogeochemistry of of phosphorus (P) in two oxic, electron donor-poor, Canadian aquifers, characterized by different aquifer material (calcareous and iron oxide-rich). The aquifer material, in particular iron oxide, is found to play a major role in the downgradient attenuation of P through sorption, whereas N, mainly in the form of NO3-, travels conservatively without major removal through denitrification. The investigation of the role of iron oxides in controlling phosphate concentrations is then extended to a subterranean estuary subject to saltwater intrusion. The behaviour of P along physico-chemical gradients of ionic strength and pH which develop during estuarine mixing, is simulated using an electrostatic surface complexation model (SCM) coupled to a 2D variable-density finite-element RTM. The transient evolution of phosphate sorption upon saltwater intrusion in a coastal aquifer and the subsequent mobilization of phosphate related to the sharp increase in groundwater pH are investigated. In many coastal aquifers, the sorption capacity of phosphate is related to the occurrence of zones of iron oxide accumulation, often referred to as “Iron Curtains”. The mechanism which drives the formation of such an “Iron Curtain” in the mixing zone of Waquoit Bay, MA, USA and the subsequent attenuation of P are studied. A 2D density-dependent flow coupled to a biogeochemical model is then applied to the extensive field data along a beach transect in the same study site, to help unravel the nutrient biogeochemical dynamics in this subterranean estuary. Results show that the conditions required for denitrification are not met and thus, SGD in Waquoit Bay is mainly a source of NO3- to the coastal zone. As illustrated by this field study, redox conditions strongly determine the extent of nutrient transformation/removal in subterranean estuaries. Therefore, four generic model subterranean estuaries, representing the end members of oxic/anoxic aquifer and seawater redox conditions are defined, to investigate further the role of organic matter reactivity, alternative denitrification pathways, as well as groundwater flow velocity and transverse dispersivity on the nutrient distributions and fluxes to the coastal waters
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