Acoustic telemetry, a commonly used tool for examining movements and survival of aquatic species, is often applied without a comprehensive understanding of transmitter implantation effects. This can be problematic when the goal of the study is to use telemetry results to make inferences regarding broader populations. Here, we examined juvenile Chinook Salmon Oncorhynchus tshawytscha at varying time intervals after transmitter implantation to assess the behavioral implications of tagging. The following behavioral metrics in response to a novel environment were compared across treatment and control groups: time to emergence from shelter into the open portion of the test arena, rheotactic response, total activity, and rates of exploration. Tagged fish (114–132 mm FL) were tested at 0, 1, or 4 d postsurgery (day‐0, day‐1, and day‐4 groups, respectively), and their behavior was compared to that of similarly handled control fish. Emergence from refuge was the only metric that differed significantly between treatment and control groups. Fish tested on the same day as the surgery were less likely to emerge from the refuge, with only 46% of the day‐0 tagged fish emerging compared to 88, 93, and 80% of the day‐1, day‐4, and control groups, respectively. However, day‐0 fish that did emerge from the refuge had rheotactic responses, total activity, and exploration rates similar to those of fish from the other treatment and control groups. This study may have fisheries research and management implications, especially for telemetry studies and monitoring efforts. We encourage researchers using this technology to consider (1) observing a post‐transmitter‐implantation recovery period of at least 24 h prior to release, adjusting study plans and logistics accordingly; (2) applying sufficient scientific rigor to emerging tagging technology prior to wide‐scale adoption; and (3) when possible, conducting concurrent battery life and tag effects studies with any field release of tagged fishes, as differing relationships between fish size, tag size, and tagging techniques may yield variable results.