Saline intrusion has the potential to cause a number of difficulties for coastal lowlands around Australia but the negative impacts of salt intrusion is not observed in the short to medium term. In order to plan for the longer term, researchers need to accurately map the saltwater distribution in the coastline. However, an appropriate finite element solver must be selected that can allow for complexities in representing the domain and boundary conditions. Saltflow and Pde2d are two such packages studied here. A 2D mathematical coupled salinity intrusion model is solved using these packages. The performances of the packages are analysed in terms of ease of use, accuracy of simulations and capacity to represent physical processes related to the boundary conditions. Problems fundamental to the saltwater literature are solved and solutions compared under different demands states. The accuracy of simulations was compared with a semi analytical solution. Although Saltflow was favoured for solving saltwater intrusion in coastal Australian lowlands, the comparison generally highlighted several user difficulties in saltwater intrusion modelling.