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The impact of maggot mass size on body water content, net transpiration rate, and dehydration tolerance of fly pupae was examined in six species of necrophagous flies. Species that spent more time on food as larvae, produced pupae with high body water contents. Dehydration tolerance limits of pupae were modest, matching the moisture-rich conditions of decaying carrion for larvae. Protophormia terraenovae pupariates on food as it dries, and this was reflected by pupae having the highest body water content and lowest net transpiration rate. Megaselia scalaris featured the lowest body water content and highest dehydration tolerance, implying that this species is arid-suited, which matches its ability to feed and colonize on post-decay carrion. Lucilia illustris was the most sensitive to larval overcrowding, resulting in a dramatic decrease in pupal size, early dispersal from food, fed less and had fast net transpiration rates. By contrast, Lucilia sericata was the most resistant, by showing no pupal size decrease and no change in net transpiration rate. Other species were between these extremes, requiring larger maggot mass sizes to produce the effect of decreasing pupal size and increasing net transpiration rate. We conclude: (1) the pupa’s response to overcrowding and water balance profile are species-specific, varying according to pupal size and net transpiration rate as independent characteristics; (2) water balance profile of the pupae reflects the behavior and microhabitat of the larva; and (3) danger of lethal desiccation to smaller-sized pupae is circumvented by a faster developmental rate rather than enhanced water conservation.