We employed a Lagrangian-like sampling design to evaluate bacterial community composition (BCC--using temporal temperature gel gradient electrophoresis), community-level physiological profiles (CLPP--using the EcoPlate™ assay), and influencing factors in different salinity waters in the highly dynamic Patos Lagoon estuary (southern Brazil) and adjacent coastal zone. Samples were collected monthly by following limnetic-oligohaline (0-1), mesohaline (14-16), and polyhaline (28-31) waters for 1 year. The BCC was specific for each salinity range, whereas the CLPPs were similar for mesohaline and polyhaline waters, and both were different from the limnetic-oligohaline samples. The limnetic-oligohaline waters displayed an oxidation capacity for almost all organic substrates tested, whereas the mesohaline and polyhaline waters presented lower numbers of oxidized substrates, suggesting that potential activities of bacteria increased from the polyhaline to oligohaline waters. However, the polyhaline samples showed a higher utilization of some simple carbohydrates, amino acids, and polymers, indicating a shortage of inorganic nutrients (especially nitrogen) and organic substrates in coastal saltwater. The hypothesis of bacterial nitrogen limitation was corroborated by the higher Nuse index (an EcoPlate™-based nitrogen limitation indicator) in the polyhaline waters and the importance of NO(2)(-), NO(3)(-), low-molecular-weight substances, and the low-molecular-weight:high-molecular-weight substances ratio, indicated by the canonical correspondence analyses (CCAs). Our results demonstrate the important stability of microbial community composition and potential metabolic activity in the different water salinity ranges, which are independent of the region and time of the year of sample collection in the estuary. This is a quite unexpected result for a dynamic environment such as the Patos Lagoon estuary.