The estuarine system of Laguna (Santa Catarina, Brazil), composed by lagoons of Santo Antonio, Imaruí and Mirim, situated to 130 km south of Florianópolis was evaluated through the association of foraminifera and thecamoebians as biological indicator organisms. The study reveals different population density patterns reflecting the environmental conditions. It is observed the formation of 4 groups. The group representing the north of the lagoon of Imaruí and the south of the Mirim lagoon (stations 14-17) is related to low density of foraminifera and thecamoebians. In the north of the lagoon of Santo Antonio and in the south part of the lagoon of Imaruí (7-13), Ammotium salsum, Ammobaculites exigus and Gaudryina exillis dominate. The group lagoon inlet (1, 2, 4-6) is composed by the stations more influenced by saline waters, presenting the highest diversities, where Elphidium poeyanum and Saccamina sphaera dominate. The group formed by stations collected in the river D'Una, Tubarão, and Mirim lagoon (3, 18-25) presents M. fusca and species of thecamoebians as indicator of large fresh water influence. Despite high fresh water input, it was observed low efficiency in water renewal especially in the north part of the estuarine system.The estuarine system of Laguna (Santa Catarina, Brazil), composed by lagoons of Santo Antonio, Imaruí and Mirim, situated to 130 km south of Florianópolis was evaluated through the association of foraminifera and thecamoebians as biological indicator organisms. The study reveals different population density patterns reflecting the environmental conditions. It is observed the formation of 4 groups. The group representing the north of the lagoon of Imaruí and the south of the Mirim lagoon (stations 14-17) is related to low density of foraminifera and thecamoebians. In the north of the lagoon of Santo Antonio and in the south part of the lagoon of Imaruí (7-13), Ammotium salsum, Ammobaculites exigus and Gaudryina exillis dominate. The group lagoon inlet (1, 2, 4-6) is composed by the stations more influenced by saline waters, presenting the highest diversities, where Elphidium poeyanum and Saccamina sphaera dominate. The group formed by stations collected in the river D'Una, Tubarão, and Mirim lagoon (3, 18-25) presents M. fusca and species of thecamoebians as indicator of large fresh water influence. Despite high fresh water input, it was observed low efficiency in water renewal especially in the north part of the estuarine system.