Natural and human-induced disturbances across aquatic and terrestrial habitats affect a broad range of species and communities causing declines in both biodiversity and population abundance. Whilst habitat disturbances are known to affect species’ distributions, phenology and physiology, less is known about the effects on development and stress physiology, especially for marine species. We investigated how a range of disturbances, mainly anthropogenic, affected the development and stress physiology of different tropical marine species. We will describe how two different habitat disturbances, the 1998 global bleaching event that reduced live coral cover and chronic boat noise, increased levels of the teleost stress hormone, cortisol in the skunk anemonefish and three-spot damselfish respectively. We will also describe how shark- and ray-feeding dive sites interact with insulin and gonadal steroid hormones of the black-tipped reef shark. Finally, we will describe how chronic boat noise slows sea hare embryonic development and reduces veliger hatching success. We will discuss how these varying habitat disturbances could impact reproduction and survival, highlighting their consequences for population dynamics.