There are more than a thousand karst ponds and several wetlands on the Istrian peninsula. Together with four small rivers and a reservoir, they form the only surface freshwater in the region. These small water bodies are generally artificial or partially modified by people who have relied on them throughout history, mainly for agricultural and livestock activities. Puddles and wetlands have also been a problem for human health in the past, favoring mosquito breeding and malaria diffusion, and were therefore massively treated with insecticides or artificially linked to the sea in the early 20th century. Nowadays, ponds are often abandoned and prone to degradation due to lack of maintenance and vegetation growth. Moreover, they often accumulate agricultural and urban water, and with it microbiological and chemical contaminants. Surface water bodies in the Mediterranean area are crucial for the survival of the surrounding terrestrial flora and fauna. In addition, they act as foci of aquatic biodiversity that provide the only refuge for various endemic species and are very important for migratory birds that play a key role in ecosystem networking and thus contribute to the conservation of southern European biodiversity. The aim of this study was to examine habitat characteristics, microbiological and sanitary conditions and traces of inorganic pollutants in the waters of five ponds and one brackish wetland in the southwestern part of the Istrian peninsula. This research provided the first data on the status of these sensitive and valuable environments, which will be the basis for the implementation of their future conservation and sustainable management programs.