A negative correlation between the degree of fine sediment deposition and the abundance of stream benthic fishes has often been reported, although the causal mechanisms for this effect are not fully understood. To better understand the influence of sedimentation, it is important to clarify whether it alters the habitat required by fish, or merely preferred by them. We conducted two enclosure experiments in the field to examine (i) whether an endangered benthic fish, Cobitis shikokuensis, prefers sediment‐free substrate and (ii) whether fine sediment deposition has negative effects on the physiological condition of C. shikokuensis. The first experiment, which used three types of substrates, ‘cobble’, ‘pebble’ and ‘mixture of fine sediment and pebbles’, showed that C. shikokuensis avoided the mixture. The second experiment, which compared the physiological condition of fish reared in enclosures with either a pebble or mixture substrate, showed that the condition of the fish in the latter group declined more quickly. These results suggest that, for C. shikokuensis, sediment‐free substrate is a habitat requirement, not merely a preference, and that excessive input of fine sediment due to human activities can cause a decline in the population of this species.
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