The distribution of the bathypelagic perch Perca fluviatilis fry (BPF) layer and its qualitative and quantitative changes were studied along the longitudinal profiles of the large canyon-shaped Slapy and Orlík Reservoirs (Czech Republic), using acoustic methods (SIMRAD EY500 echosounder, split-beam transducer, Sonar5 post-processing software). In Slapy Reservoir (sampled in late May), the BPF layer created by the mass of non-shoaling perch larvae and juveniles (average total length, LT, 10·4 mm) was recorded from the dam for 29 km upstream. The BPF layer only vanished in the upper third of the reservoir due to the extremely cold hypolimnetic water discharged from Orlík Reservoir, which is situated upstream in the cascade. Both abundance and size of BPF increased significantly upstream following, in Slapy Reservoir, the trophic gradient. In Orlík Reservoir (sampled in late June), the BPF layer was created predominantly by shoaling perch fry individuals (average LT 31·8 mm), recorded along the whole longitudinal profile of the reservoir (>50 km, filled with relatively warm water). Both the sizes of BPF and their shoaling activity again increased significantly from the dam towards the inflow following, in Orlík Reservoir, the trophic gradient. Pooling the data from both reservoirs, it was evident that the tendency to flock in a dense layer and, much later, to create distinct shoals, increased continuously with the size of BPF. A number of variables describing the BPF layer in Slapy and Orlík Reservoir are given.