The objective of the studies presented in this thesis is to use modelling and experimental analyses to elucidate the important processes and mechanisms affecting contaminant transport in various groundwater systems and to establish values of transport parameters that could be used to describe these processes. The important contaminant transport processes and mechanisms explored in these studies include scale-dependent dispersion, interaction between sorption and first-order degradation, effects of pore-water velocity on chemical-non-equilibrium sorption, degradation and sorption of pesticides, die-off and filtration of microbes, and velocity-enhanced microbial transport (i.e. faster transport of microbes than conservative solute tracers). Specifically, this thesis includes studies which (1) develop and validate solutions for a scale-dependent dispersion model, (2) validate a novel method of temporal moments, (3) model non-equilibrium transport of Cd, Zn and Pb in an alluvial gravel aquifer medium, (4) explore attenuation and transport of atrazine, hexazinone, procymidone, faecal bacteria and F-RNA phages in pumice sand aquifer media, (5) quantify setback distances between septic tanks and the shoreline of Lake Okareka based on transport of microbial indicators in a pumice sand aquifer and worst-case values for aquifer properties and effluent discharge, (6) introduce methods related to modelling non-linear equilibrium sorption, and (7) discuss other important issues involving contaminant transport in groundwater (e.g. preferential flow, maximum groundwater velocity, velocity enhancement due to size/anion exclusion) as well as issues related to contaminant transport modelling. By calibrating a number of transport models with observed data, we have obtained descriptive parameters that characterize contaminant attenuation and transport in the selected aquifer systems. The methods presented in this work will allow researchers and groundwater resource managers to better understand, and therefore quantitatively predict, the fate and transport of contaminants in the subsurface. In addition, gaps in the current literature that are identified in this thesis and some of the ideas presented herein could be used for planning future research.