Sensors such as electrodes and optical fibre devices, optrodes, can be used to determine steep concentration gradients of chemical species in aquatic microenvironments, such as in the pore waters of surface sediments and microbial mats, but are limited to a restricted range of determinands. The highest-resolution measurements of trace-metal concentrations in pore waters, at about 1.25 mm, have been provided by a recently developed thin- film gel technique, but the resultant metal distributions suggest that sub- millimetre-scale gradients need to be determined if the fluxes and cycling of the metals are to be fully quantified and understood. Here we report the development of this thin-film gel technique to measure Zn, Mn, Fe and As fluxes and concentrations at a resolution of 100 μm, and demonstrate the utility of the method in situ within the surface sediments and overlying microbial mat of a stream. Vertical profiles through the mat and sediments, and horizontal two-dimensional mapping just below the sediment-water interface, reveal the contrasting the gradients, fluxes and remobilization niches of the four metal species at a submillimetre scale. The microbial mat appears to be an important regulator of the cycling of these metals. This technique has the potential to be extended to other chemical species and applied to other microenvironments with steep concentration gradients, such as redox boundaries, plant roots, animal burrows and sites of precipitation/dissolution in soils and sediments.