**Abstract**

The chapter is about the study of environmental conditions and the structure of the benthic diatoms community in Peixe Lagoon, which is inserted in a National Park in southern Brazil. The study was carried out covering four seasons from 2011 to 2012. The system is shallow (<60 cm) located parallel to the coastline, and it is connected to the ocean through a single channel, which occurs naturally or through human action. In this lagoon, during the study, the water temperature ranged between 15.3 and 32.1°C, and the dissolved oxygen presented higher value in the winter (12.5 mg.L<sup>−</sup><sup>1</sup> ) and lower value in the summer (7.5 mg.L<sup>−</sup><sup>1</sup> ). The lagoon ranged from mesotrophic to hypereutrophic conditions. The salinity varied between 1.3 and 36.2%, and these variations were mainly related to meteorological conditions. The community of diatoms in Peixe Lagoon is composed by 62 taxa distributed in 30 genera composed largely of marine, brackish, and few freshwater species. Among the attributes of the community, composition better reflects the environmental variations. The opening and closing of the channel, salinity, temperature, and the action and direction of the wind are variables influencing the dynamics of the microphytobenthic community.

**Keywords:** environmental variables, diatoms, community attributes, microphytobenthos, system dynamic
