Groundwater-dominated streams have particular flow regimes that commonly support populations of trout. Meso- and micro-habitat surveys were carried out on a reach of the river Tern that drains a Triassic sandstone aquifer in the English West Midlands, to investigate brown trout (Salmo trutta) habitat use with varying flows. Mesohabitats were mapped over a range of summer and autumn flows and coupled with direct underwater observation (snorkelling) of fish locations together with point measurements of velocity and depth. The number of habitat types recorded was low and dominated by glides, runs, and backwaters. Brown trout showed a strong association with glides and runs with adults being more associated with runs and parr with glides. General habitat use curves showed brown trout to favour depths between 0.30 and 0.40 m and velocities below 0.40 m s−1. A clear preference was shown for sand and gravel bed materials. However, the differentiation of hydraulic habitats was weak and there was no trend in mesohabitats or change in trout use of mesohabitats with discharge. The study raises limitations of the mesohabitat survey approach when linking fish ecology, flow and physical habitat in small streams with low flow variability and low habitat diversity. In these situations, other factors (especially cover features) appear to strongly influence brown trout distribution.