Each year, thousands of fishes are tagged with electronic devices to study their biology and inform fisheries management. Such research assumes that the process of capturing, tagging, and then holding fish to allow them to recover before release (i.e., the “tagging process”) does not alter the physiology, behavior, and survival of these fish. However, the fish can experience physiological challenges during the tagging process that may affect their behavior and survival. We have observed that the rationale used to establish protocols for holding durations and conditions of fish before and following surgery has received little attention. Here, we provide a perspective that: (1) provides an overview of the tagging process and its effects on the physiology, behavior, and survival of fish; (2) highlights the diverse holding conditions and durations used by researchers (that are often inadequately described and seem arbitrary); and (3) identifies key research needs. We conclude that decisions of whether, how, and for how long to hold tagged fish before release depend on diverse circumstances that need to be evaluated by researchers. We recommend that researchers explicitly report the details of how, when, where, and why tagged fish are held to facilitate protocols that benefit fish welfare, science, and management.