Most reactive transport models have represented sediments as one-dimensional (1-D) systems and have solely considered the development of vertical concentration gradients. However, application of recently developed micro-scale and 2-D measurement techniques have demonstrated more complicated solute structures in some sediments, including discrete localized sites of depleted oxygen, and elevated trace metals and sulphide, referred to as microniches. A model of transport and reaction in sediments, that can simulate the dynamic development of concentration gradients occurring in 3-D, was developed. Its graphical user interface (GUI) allows easy input of user-specified reactions and provides flexible schemes that prioritise their execution. The 3-D capability was demonstrated by quantitative modelling of hypothetical solute behaviour at organic matter microniches covering a range of sizes. Significant effects of microniches on the profiles of oxygen and nitrate are demonstrated. Sulphide is shown to be readily generated in microniches within one centimetre of the sediment surface, provided the diameter of the reactive organic material is greater than one millimetre. These modelling results illustrate the geochemical complexities that arise when processes occur in 3-D and demonstrate the need for such a model. Future use of high-resolution measurement techniques should include the collection of data for relevant major components, such as reactive iron and manganese oxides, to allow full, multi-component modelling of microniche processes.