Mangroves are considered as natural nurseries and classified as permanent protected areas. The study area is the municipal ecological site of Ilha do Lameirão, covering 891.83 ha of mangrove forest. This area persistently suffers from anthropic pressure. For this reason, there is the need to study and monitor the microbiological characteristics and recognition of the main factors involved in the degradation of mangroves process. This study was done in the year 2014. Samples were taken every month during dry and rainy seasons. Two areas (Maria Ortiz and Canal dos Escravos) were chosen based on the degree of their vulnerability to anthropic pressure. The results show there is a microbiological contamination both in water and Crassostrea rhizophorae tissues, mainly in samples taken from Maria Ortiz. According to the results, the Canal dos Escravos estuary, known as Class 1 is an environment that is able to maintain aquatic communities and fishing activities. In oyster tissues, microorganism strains that indicate the pathogens which cause diseases in humans were identified.