Managed Aquifer Recharge (MAR) is becoming an increasingly attractive water management option, especially in semiarid areas. Nevertheless, field studies on the fate and transport of priority substances, heavy metals and pharmaceutical products within the recharged aquifer are rare. Based on the above, the objective of this project is to study the hydrological conditions of the coastal aquifer of Ezousa (Cyprus) and its ability to attenuate pollutants. The Ezousa riverbed is a locally important aquifer used for a MAR project where treated effluent from the Paphos Waste Water Treatment Plant is recharged into the aquifer through a number of artificial ponds along the riverbed. Additionally, groundwater is pumped for irrigation purposes from wells located nearby. The hydrological conditions of the area are unique due to the construction of the Kannaviou dam in 2005 that reduced natural recharge of the Ezousa aquifer significantly, inducing the saltwater intrusion phenomenon. A three-dimensional finite element model of the area was constructed using the FEFLOW software to simulate the groundwater flow conditions and transport of Phosphorous and cooper in the subsurface from the recharge process. The model was calibrated using hydraulic head and chemical data for the time period of 2002-2011. The groundwater model was coupled with a geochemical model PHREEQC attempting to evaluate nitrate and Copper processes. Inverse modeling calculation was used to determine sets of moles transfers of phases that are attributed to the water composition change in groundwater between the mixture of natural groundwater and reclaimed wastewater and the final water composition.