Globally estuaries are under increasing pressure from human development impacts including the growing effects of climate change that already cause major changes in freshwater inflow. One of these are drought events. Although they are regular occurrences and are projected to become progressively more significant in many parts of the world, their realised impact on the estuarine biome requires better understanding and quantification. In this study, we analysed the environmental niche variability along horizontal and vertical estuarine axes during the dry and wet season of a drought and non-drought period, in two contrasting subtropical estuary types in South Africa: the temporarily closed uMdloti Estuary and the predominantly open uMlalazi Estuary. We found quantitative support for the hypothesis that extended periods of drought lead to a decreased niche availability for estuarine organisms over both space and time, expressed as narrower salinity ranges, less habitat with amicable dissolved oxygen (DO) concentrations, and more frequent higher temperature. Drought caused a more homogenous salinity environment in both estuaries, more specifically extremely low salinity throughout the temporarily closed estuary, but increased salinity in the predominantly open estuary. DO levels were more variable during drought conditions and included periods of hypoxia in both estuaries. They were more stable at elevated levels (>5 mg/L) during non-drought conditions. The opposite was true for pH, for which we measured lower values and larger vertical ranges during non-drought conditions when rainfall and tidal exchange were more pronounced. Higher temperature value density peaks were apparent from the drought period, especially pronounced in the temporarily closed uMdloti Estuary. The physico-chemical environment was typically more estuarine during the non-drought period, and drought caused both similar (temperature, DO, pH) and different (salinity) responses in the two estuarine types. Drought-induced conditions can span several generations for estuarine and estuarine-associated species. It is important to quantify niche variability for a range of estuary types to subsequently understand drought effects on estuarine biodiversity.