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The impact of preferential pathways for groundwater movement on wetland function was studied in the riparian system associated with a first-order stream draining an agricultural catchment. Evidence for preferential groundwater flow includes finding open macropores and layers of wetland soil with high hydraulic conductivity. These flow pathways were found to operate on different orders of scale within the wetland ecosystem. Open channel macropores in the system typically function on a relatively small (centimeter) scale as determined by pore diameter and length. Larger orders of scale include the continuous layers of high-conductivity material which can operate with meter-plus dimension. The range of hydraulic conductivity can span three orders of magnitude (10-4 to 10-7) within typical profiles of the wetland soil, which provides a strong tendency for preferential movement of water through sections of high conductivity. Biological activities are also highly stratified in these profiles with the highest activity occurring in the upper portion of profile that receives organic residue from wetland vegetation. The prevalent movement of groundwater by preferential flow pathways in conjunction with strong anisotropic structure of biological activities, such as denitrification, suggests that strong spatial components within wetland ecosystems may limit their ability to mitigate agricultural pollutants. Concentrated flow of water limits both residence time and degree of interaction with biologically active zones, with possible bypass of zones with greatest ability to remove pollutants.