<p>Marine protected areas play a growing role in conservation and fisheries management, though they remain controversial. Early theoretical work, based on analyses of population dynamics at stable equilibrium states, suggested that the implementation of marine protected areas could contribute to multiple goals such as maintaining species persistence (conservation goals) and maintaining or increasing fishery yields (fisheries goals), even—under some conditions—exceeding outcomes from conventional (i.e., non-spatial) management strategies. However, more recent work has recognized that when protected areas are first established, the newly protected populations may be far from their eventual equilibrium state, leaving managers to contend with “transient” dynamics as the system moves towards that equilibrium state over years or decades. Here, we review the development of our understanding of those transient dynamics from models, and how that understanding can improve protected area management for both fisheries and conservation goals. The extent to which fish population varies in transient time scales depends on life histories (e.g., reproduction, survival, and fishing mortalities) and the measurement of yield judged by either biomass or number, and the order in which closures are implemented over time for interacting species. Understanding transients also helps set realistic expectations for adaptive management by allowing more accurate predictions of the magnitude of protected area effects on previously fished populations over short time scales. Continuing to consider transient population dynamics will benefit policy-makers in both conservation and economic goals by providing a stronger theoretical foundation for adaptive marine protected area management.</p>