Population control in some form of harvesting might be expected to reduce population size, but quite the opposite can happen due to the hydra effect. This phenomenon describes an increase in population size with increased mortality. One mechanism causing hydra effects is the temporal separation of (i) harvesting and (ii) density-dependent reproduction. Here we consider discrete-time models of these two processes. It is commonly believed that harvesting needs to precede reproduction for a hydra effect to occur. We show that, by contrast, hydra effects also take place for harvest after reproduction. Due to the timing of population census, however, the hydra effect will not be measured and thus remains ‘hidden’. As a consequence, managers may miss out on the opportunity to increase both the yield and the remaining stock of renewable resources. If harvesting aims at controlling pest species, management interventions may backfire in the sense that the pest increases rather than decreases—and, to make things even worse, this may actually go unnoticed. To remedy these undesirable consequences, we propose a modelling framework that can reveal hidden hydra effects. Our results are based on rigorous mathematical proofs that the order of two events does not matter for standard harvesting/hunting strategies.