Environmental context. Modelling of discrete sites of diagenesis in sediments (microniches) has typically been performed in 1-D and has involved a limited set of components. Here we present a new 3-D model for microniches within a traditional vertical sequence of redox reactions, and show example modelled niches of a range of sizes, close to the sediment–water interface. Microniche processes may have implications for understanding trace metal diagenesis, via formation of sulfides. The model provides a quantitative framework for examining microniche data and concepts. Abstract. 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 microscale and 2-D measurement techniques have demonstrated more complicated solute structures in some sediments, including discrete localised sites of depleted oxygen, and elevated trace metals and sulfide, 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 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. Sulfide is shown to be readily generated in microniches within 1 cm of the sediment surface, provided the diameter of the reactive organic material is greater than 1 mm. 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, multicomponent modelling of microniche processes.