<p>In coastal aquifers, we face the problem of salt water intrusion, which creates a complex flow field. Many of these coastal aquifers are also exposed to contaminants from various sources. In addition, in many cases there is no information about the characteristics of the aquifer. Simultaneous identification of the contaminant source and coastal aquifer characteristics can be a challenging issue. Much work has been done to identify the contaminant source, but in the complex velocity field of coastal aquifer, no one has resolved this issue yet. We want to address that in a three-dimensional artificial coastal aquifer.</p><p>To achieve this goal, we have developed a method in which the contaminant source can be identified and the characteristics of the aquifer can be estimated by using information obtained from observation wells. First, by assuming the input parameters required to simulate the contaminant transfer to the aquifer, this three-dimensional coastal aquifer that is affected by various phenomena such as seawater intrusion, tides, shore slope, rain, discharge and injection wells, is simulated and the time series of the output parameters including head, salinity and contaminant concentration are estimated. In the next step, with the aim of performing inverse modeling, random values &#8203;&#8203;are added to the time series of outputs obtained at specific points (points belonging to observation wells) in order to rebuilt the initial conditions of the problem to achieve the desired unknowns (contaminant source and aquifer characteristics). The unknowns estimated in this study are the contaminant source location (x, y, z), the initial contaminant concentration, the horizontal and vertical hydraulic conductivity of the aquifer. SEAWAT model in GMS software environment has been used to solve the equations of flow and contaminant transfer and simulate a three-dimensional coastal aquifer. Next, for reverse modeling, one of the Bayesian Filters subset (ensemble Kalman filter) has been used in the Python programming language environment. Also, to reduce the code run time, the neural network model is designed and trained for the SEAWAT model.</p><p>This method is able to meet the main purpose of the study, namely estimating the value &#8203;&#8203;of unknown input parameters, including the contaminant source location, the initial contaminant concentration, the horizontal and vertical hydraulic conductivity of the aquifer. In addition, that makes it possible to achieve a three-dimensional numerical model of the coastal aquifer that can be used as a benchmark to examine more accurately the impact of different phenomena simultaneously. In conclusion, we have developed an algorithm which can be used in the world's coastal aquifers to identify the contaminant source and estimate its characteristics.</p><p>&#160;</p><p>Key words: coastal aquifer, seawater intrusion, contaminants, groundwater, flow field, parameter estimation, ensemble kalman filter</p>