There is an increasing need to understand the behaviour of engineered earth systems, from the viewpoint of safe waste disposal and exploration of renewable energy sources. Often, human activities lead to significant perturbations of the earth systems, involving hydrologic, mechanical, thermal and chemical processes. Prediction of the long-term response of earth systems to large perturbations is critical for evaluating their design, performance and operation. Because many of the processes involved in system response will manifest over decades or centuries, field-testing during the design stage is infeasible. In this connection, we propose that development of coupled process simulators and testing them on natural analogs provided by geologic systems may be fruitful. As example, we illustrate our attempts to simulate the development of two types of cave systems - branchwork in meteoric environments and mazework in hypogene or hydrothermal environments. Our computational models combine hydraulic, thermal and chemical processes in limestone fractures and consider the influence of subsurface heterogeneity as well. Our computational results vividly demonstrate the mechanisms by which branchwork patterns develop in meteoric environments and demonstrate how sustained dissolution along upward flow channels can be established in hypogene environments, thus creating favourable conditions for development of maze patterns. Investigations of system sensitivities in both types of environments indicate that a surprisingly robust pattern of behaviour results, thus serving as a target for developing simplified conceptual models of these systems. We also discuss the implications of our results for design, operation and risk analysis of engineered earth systems.