The effects and consequences of changes in thyroid hormones (THs) level are among the actively studied topics in teleost developmental and evolutionary biology. In most of the experimental models used, the altered hormonal status (either hypo- or hyperthyroidism) is a stable characteristic of the developing organism, and the observed phenotypic outcomes are the cumulative consequences of multiple TH-induced developmental changes. Meanwhile, the influence of the transient fluctuations of TH content on skeleton development has been much less studied. Here, we present experimental data on the developmental effects and phenotypic consequences of transient, pharmacologically induced thyrotoxicosis and hypothyroidism at different stages of ossified skeleton patterning in zebrafish. According to the results, the skeleton structures differed in TH sensitivity. Some showed a notable shift in the developmental timing and rate, while other demonstrated little or no response to changes in TH content. The developmental stages also differed in TH sensitivity. We identified a relatively short developmental period, during which changes in TH level significantly increased the developmental instability and plasticity, leading to phenotypic consequences comparable to those in fish with a persistent hypo- or hyperthyroidism. These findings allow this period to be considered as a critical developmental window.