The swimming performance of two fish species having initially different swimming strategies, brown trout and whitefish, was measured after training in order to relate the effects of exercise on calcium handling and muscle performance of fish. The time to 50% fatigue was measured during the training period, and compared with the density of dihydropyridine (DHP) and ryanodine (Ry) receptors determined by histochemical analysis from swimming muscles. Overall, both trained brown trout and whitefish had superior swimming performance as compared to control ones. Interestingly, brown trout achieved the highest swimming performance swimming against the water flow velocity of 2 BL/s while among whitefish the best efficiency was seen after training with lower swimming velocities. Training also induced a significant increase in DHP and Ry receptor density in both species. Generally, in brown trout the most notable increase was observed in red muscle sections from the fish swimming for six weeks against water currents of 1 BL/s (DHPR 176.57.7% and RyR 231.411.8%) and white muscle sections against 2 BL/s (DHPR 129.612.4% and RyR 161.915.5%). In whitefish the most prominent alterations were noted in samples from both muscle types after six weeks of training against water current of 1.5 BL/s (DHPR 167.116.9% and RyR 190.419.4%). To conclude, our findings demonstrate an improved swimming performance and enhanced calcium regulation after training. Moreover, there seems to be a connection between the swimming performance and receptor levels especially in white swimming muscles of different fish species, regardless of their initially deviant swimming behaviours. However, depending on the training regimen the divergent swimming behaviours do cause a different response.