Spatial heterogeneity among microhabitat patches in aquatic ecosystems creates refuges (e.g., substrate interstices) that protect organisms against a variety of environmental constraints. Aquatic insects have evolved the ability to alter their life-history traits in response to environmental variability. Our objective was to determine whether differences in hydraulic and substrate conditions cause phenotypic plasticity in nymphs of the stonefly Nemoura cinerea Retzius. We experimentally manipulated near-bed current velocities (3 and 9 cm/s) and substrate types (medium sand and coarse gravel) in indoor artificial channels. Changes in the head capsule width, mesothoracic wing pad length, total body length, body mass, and behavior were studied over a 4-wk period. Morphometric and behavioral differences were primarily associated with the mechanism of refugium use (although confounded by substrate size), which reduced energy expenditure. Growth (body size and mass) was reduced in sand (absence of refugia) relative to growth in gravel, regardless of current velocity, and nymphs made almost no investment in body length (variation in allometry). The effect of current velocity on behavior was less marked in sand than in gravel because of a possible confounding effect of direct exposure of nymphs to flow on sand (i.e., no available refugia). In sand, individuals were located mainly on the food source (erect leaf discs) at current velocities of 3 cm/s, but feeding was depressed. Therefore, nymphal development was slow on sand. In gravel, nymphs followed different developmental trajectories depending on current velocity because hydraulic stress seemed to trigger accelerated development. Our study shows that physical factors associated with habitat structure can result in adaptive phenotypic plasticity among aquatic insect populations, and that a lack of shelter might have a strong impact on stonefly fitness.