This study uses a fieldwork-modelling research methodology to investigate hydrological pathways and chemical transport in floodplains and riparian zones, which occupy a key position in the landscape at the catchment-river interface. A numerical model is developed (ESTEL2D-SUBIEF2D) that is capable of modelling subsurface water and chemical movement at a high spatial and temporal resolution. The model is used in conjunction with data from two field sites (a lowland floodplain on the River Severn, UK, and a headwater riparian zone on Sleepers River, USA), and with hypothetical tracers, to quantify the effect of a range of factors on the operation of hydrological and biogeochemical processes in floodplain systems. This study shows the relative importance of river and hillslope inputs of water and chemicals to the floodplain, and how the scale of hydrological event (overbank flow, bankfull flow and low flow) affects the interaction of these sources. For example, in the case of an overbank flood event, hillslope inputs can be held back by the steep hydraulic gradient induced by flood water for up to 10 days. A comparison of headwater and lowland floodplains is attempted for the first time and indicates that different hydrological processes operate in these two environments. This implies that results from existing smaller scale riparian zone studies cannot simply be 'scaled up' to larger, lowland floodplain zones. The operation of the denitrification process within the floodplain is investigated as a relevant example of the more general transport modelling capability of the numerical code. This supports and extends the results of previous studies which have suggested that denitrification in the floodplain may be fundamentally limited by the interaction of hydrological processes and carbon availability. This comprehensive exploration of the full range of subsurface flow pathways through the floodplain highlights the importance of an understanding of hydrological pathways as critical to understanding chemical transport within the floodplain system.