Electrofishing surveys provide important information on watershed health, and the status of imperiled and recreationally important stream fishes. Concerns about the harmful effects of electrofishing on the endangered redside dace Clinostomus elongatus have resulted in restrictions on its use in sampling activities in the province of Ontario, Canada. However, the effectiveness of these restrictions is unproven. We undertook a paired sampling gear study in 2018-2019 to test whether an alternate gear (seine nets) or a change in electrofishing timing (autumn rather than summer) reduced harm to stream fishes. The study took place in streams located in the Greater Toronto Area. We found large differences in the frequency and magnitude of sampling-related mortalities between sampling gear and seasons. During individual surveys, electrofishing mortality never exceeded 9% in the summer or 4% in the autumn, while seining-related mortality reached 60% at two stream sites. Overall, autumn electrofishing resulted in mortality rates that were 5.6 and 15 times lower than summer electrofishing and summer seining. These results indicate that survival of Ontario stream fishes can be improved by delaying electrofishing until early autumn.