Small planktonic copepods are abundant on coasts, forming the basis of food webs. Size-based normalized biovolume spectra are increasingly used to study plankton and the impacts of droughts. Biovolume is a key indicator of plankton characteristics and biomass, but research on biovolume in estuarine hypersalinity is limited. Our study estimated the biovolume and biomass of keystone tolerant species (e.g., Oithona) to assess salinity fluctuations impact in a tropical estuarine system. Copepod sampling and salinity measurements were taken bimonthly over a year during extreme drought and short rainfall events. We found higher biovolume under mild hypersalinity (similar to 48 and 55) and the lowest under meso- and eusalinity (similar to 11 and 37). The biomass responded similarly to biovolume, except in February when the biovolume was high but density was low. These variations were linked to copepod sensitivity to great salinity fluctuations. In this regard, the stress-tolerant species thrived under lower diversity and milder hypersalinity during the dry season. Great freshwater input from heavy and short rainfall represents a disturbance to keystone estuarine organisms such as Oithona spp. that face low water input and high temperatures during most of the year in a semi-arid coast. This led to a reduction in biovolume and biomass of these organisms during meso- and euhaline regimes. Our findings suggest that moderate stress conditions benefit Oithona biomass, while extreme environmental conditions (e.g., episodic floods) exceed their tolerance, providing insights into how climate change and extreme weather events may affect estuarine populations.