Soil erosion in clayey, subsurface drained agricultural fields in Finland can cause problems due to the export of suspended sediment and sediment-bound nutrients into nearby waterways. Suspended sediment is transported from the field via two main hydrological pathways: 1) surface runoff and 2) preferential flow in macropores to subsurface drains. In clayey fields especially, the sediment load via the subsurface drains can be a considerable part of the annual load. The mechanisms contributing to the sediment load during the growing season and the following autumn were quantified with a new numerical model (FLUSH) developed in the study, using sample data from two clayey, subsurface drained field sections in southern Finland. The simulated field was computationally divided into two-dimensional overland and three-dimensional subsurface domains. Existing mechanistic approaches were applied to describe both surface and subsurface domain processes in the model. A dual-permeability model can simultaneously simulate flow in both soil matrix and macropore systems. The model supports simulation of suspended sediment transport in macropores, drainage systems, soil swelling and shrinkage processes and the effects of cropping and tillage operations on water and sediment yields. A new pentadiagonal matrix algorithm-based solution was developed to directly solve subsurface flow in both pore systems. A custom time integration method was derived to run the solution algorithms with different time steps in concurrent fashion. All the finite volume-based partial differential equation solution algorithms were parallelised with the OpenMP application interface. Computational grids, created with an automatic grid generation system, were used to test the effects of grid resolution on results. The numerical model successfully described water flow and soil erosion in the study fields indicating that the hypothesised mechanisms for water flow and soil erosion were appropriate. The simulation results confirmed that preferential flow has a profound impact on field-scale hydrology. Runoff distribution between surface runoff and drainflow changed in the autumn due to tillage operations and soil swelling. Soil erosivity also increased after autumn tillage. In the simulations, hydraulic erosion was the primary process leading to high erosion rates in the Sjökulla field. In the Hovi field, lack of surface runoff notably lowered the sediment loads. Simulations with 1-D and 2-D grids indicated that the application of a 3-D model to undulating, clayey, subsurface drained fields was well justified. Tests with spatial variation of macroporosity presented evidence that the spatial variability of soil properties has a notable effect on runoff and sediment loads.