Engineered liner systems are widely used in various types of waste repositories such as municipal waste landfills, leachate ponds, remediation sites and solar and brine ponds. Designers, practitioners and regulators often need to assess the ability of actual or planned liner systems to perform their function adequately over a long time scale dictated by the slow transport properties in low-permeability soil. The flow and chemical transport equations, either independently or in coupled mode, under either saturated or unsaturated conditions, need to be solved, while incorporating complex liner details in the simulation. General-purpose finite element software able to solve these equations often are cumbersome when analysts use them to build liner systems. This paper presents a new finite element software system developed at the Centre for Geotechnical Research of the University of Sydney over the last 5 years. The software, called Soil Pollution Analysis System (SPAS), has been designed to simplify the model-building process of liner systems, while allowing for a range of flow and transport problems to be simulated in 2D and 3D. SPAS is able to solve 28 different types of coupled or uncoupled problems for water flow and single-phase, multiple-porosity chemical transport, in saturated or unsaturated media, under steady-state or time-dependent conditions. A powerful feature of SPAS is its ability to seamlessly model coupled problems in which the transport of chemical species depends on highlyheterogeneous water seepage velocity fields. Processes such as biological, radioactive or chemical decay, diffusion, mechanical dispersion, advection, sorption (linear or non-linear, instantaneous or time-dependent), multi-layering and interface partitioning can all be represented in the model. In unsaturated soils, a range of commonly used soil water characteristic curves is available. The software has been extensively validated and optimised and, in 2D, typically computes the full history of flow and contamination, in less than five minutes of computing time on a Windows-based personal computer with an i5 Intel processor.