The Convention on Wetlands or Ramsar Convention on Wetlands (Ramsar Convention Secretariat, 2016) currently includes over 2,400 Ramsar Sites around the world, which cover more than 2.5 million square kilometers (Ramsar, 2023a). In Brazil there are 27 Ramsar sites, which are priority wetlands areas for international conservation (Ramsar Sites Information Service, 2023). In São Paulo State, the Cananéia-Iguape Estuarine-Lagoon Complex (CIELC) integrates the Cananéia-Iguape-Peruíbe Environmental Protection Area (CIP-EPA) as a Biosphere Reserve (UNESCO) (ICMBio, 2020) and, in 2017, it was included in the Ramsar list of wetlands of international importance (Ramsar, 2017), which makes it a priority area for conservation.Conservation units are constantly subject to the input of organic and inorganic compounds related to natural disturbances such as tidal dynamics, rainfall, storms and hurricanes, and to anthropogenic activities such as sewage disposal and engineering works. These issues generally modify hydrobiogeochemical characteristics and processes and, as a long-term consequence, promote restrictive and/or adverse effects on living organisms by changing their ecophysiological responses. In this context, this special issue aims to present various scientific studies carried out in the CIELC, covering aspects of water chemistry