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Summary 1. The spatial heterogeneity of ecosystems as well as temporal activity patterns of organisms can have far-reaching effects on predator–prey relationships. We hypothesised that spatiotemporal constraints in mesohabitat use by benthic fish predators would reduce habitat overlap with benthic invertebrates and lead to mesohabitat-specific predation risks. 2. We analysed the spatiotemporal activity patterns of two small-bodied benthivorous fishes, gudgeon (Gobio gobio) and stone loach (Barbatula barbatula), and of benthic invertebrates in a small temperate stream during three 24-h field experiments. By applying a novel method of field video observation, we monitored the spatiotemporal foraging behaviour of the fish in their natural environment. A parallel analysis of invertebrate mesohabitat use by means of small area Hess sampling allowed a direct estimation of habitat overlap at a pool–riffle scale. 3. Gudgeon showed a dominant spatial activity pattern preferring pools at all times of day, whereas stone loach used both mesohabitats but with a distinct temporal (nocturnal) activity pattern. The patterns of residence were not identical with those of active foraging. Invertebrate community composition differed significantly between mesohabitats but not between times of day. More than half of the total dissimilarity between pools and riffles was accounted for by six invertebrate taxa. Five of these were subject to higher fish predation in pools than in riffles. The total prey consumption of the two fish species together in pools was about three times as high as in riffles. Trophic niche breadth of stone loach and thus its predation range was broader than that of gudgeon. 4. These results indicate that the potential predation risk for stream invertebrates depends on the combination of spatial and temporal patterns of both predator and prey. Given the distinct differences in predation risk found between pools and riffles, we conclude that spatial heterogeneity at the mesohabitat scale can influence mechanisms and consequences of selective predation. We also suggest that the analysis of spatiotemporal predator–prey relationships should not be based on the premise that the main residence habitat and active foraging habitat of a predator are identical.