Problems of investigative methodology comprise a critical and often preponderant element of research to delineate and quantitate processes which govern the transport and fate of pollutants in subsurface environments. Examination of several recent research studies illustrates that both laboratory and field (in-situ) methodologies are useful in subsurface processes research, but also clearly shows that such research involves formidable methodological problems which result primarily from the nature of terrestrial subsurface environments. This causes major methodological problems in acquiring authentic, uncontaminated samples of water and/or solids for analysis and microcosm construction. Subsurface environments are also highly structured and often exhibit significant heterogeneity across relatively short distances, which causes difficulties in determining proper locations for sample acquisition and in simulating subsurface environments in the laboratory. Advances in a number of diverse areas, including particularly geophysical methods, analytical procedures, microcosm technology, and drilling, coring, and well completion techniques, are required for needed improvements in methodology for subsurface processes research.