Hydropower development poses severe threats to the aquatic diversity and ecosystem services. One such threat is the exposure of fish to extreme conditions within hydropower facilities. Fish may suffer rapid decompression when passing through turbines or when entering the draft tubes, which can lead to barotrauma and mortality. We aimed to evaluate the effects of rapid decompression on the Amazonian benthic species Pimelodus pictus (Pictus catfish), by simulating in hypo-hyperbaric chambers. The most frequent injuries in Pictus catfish exposed to simulated rapid decompression were swim-bladder rupture, intestine rupture, internal haemorrhage and embolism. The occurrence and magnitude of internal haemorrhaging and emboli were related to the ratio of pressure change and the decompression timespan, whereas swim-bladder rupture occurred even at relatively low ratios. Emboli was present almost entirely among fish with a ruptured swim bladder. Importantly, all fish were negatively buoyant before exposure to decompression, posing challenges to data analysis. Therefore, barotrauma studies with benthic fish species are deemed to be challenging and are likely to require the use of complementary approaches. Research is needed to understand the state of buoyancy of benthic fish in the wild and to develop methods to accurately replicate these in a controlled testing environment.