Performing fish survey protocols with different electrofishing equipment and settings can lead to difficulties in comparing the data obtained. In this study, we captured two fish taxa (i.e. the European eel and salmonids: Atlantic salmon and brown trout) in the field using four models of electrofishers that provided different waveforms: direct current (DC), pulsed direct current (PDC) and pulsed exponential current (PEC). This study aimed to assess effects of using different waveforms and frequencies, while considering environmental variables, on i) attraction, represented by occurrence and catch-per-unit-effort (CPUE) of fishes, and ii) spinal damage, based on ultrasound of the spinal column. For all species, DC and PDC yielded equivalent occurrences and CPUEs, regardless of the frequency. In contrast, PEC induced a significant decrease in occurrences and CPUEs of both eels and salmonids. The percentage of injured fishes increased as the frequency or length of the salmonids increased while waveform had no effect. Ultrasound was determined to be a good non-invasive method to detect injuries in fishes.