A study on the bacterioplankton of Conceição Lagoon (27 degrees 34' S-48 degrees 27' W), Southern Brazil, was carried out in July 2005 (austral winter) and January 2006 (austral summer) to characterize the bacterial spatiotemporal distribution and to determine the heterotrophic and photoautotrophic bacterial dominance in hypoxic/oxic stratified waters. Bacterial abundance increased significantly (p < 0.05) in summer with averages of coccus cyanobacteria (CCY) ranging from 1.02 x 10(5) (winter) to 3.21 x 10(6) cells mL(-1) (summer), heterotrophic coccus/rod-shaped (HCR) cells from 7.00 x 10(4) to 3.60 x 10(6) cells mL(-1), and heterotrophic filamentous (HF) bacteria from 2.90 x 10(3) to 2.74 x 10(5) cells mL(-1). Bacterial biovolumes also increased in summer with mean biovolumes of CCY ranging from 0.38 to 1.37 microm3, HCR cells from 0.31 to 1.12 microm3, and HF from 3.32 to 11.34 microm3. Principal component analysis showed that salinity, temperature, and light were the abiotic factors that better explained the temporal variability of bacterial assemblages. Bacterial heterotrophy dominated in the lagoon, excepted by the southern and part of central sector in January 2006, when autotrophic-dominated microbial community occurred. Spatially, bacterial assemblages were influenced by nutrient gradient, oxygen, and salinity with a positive relationship between biovolumes and nutrients and a negative relationship between abundance of coccus cyanobacteria and nutrients. The stratified [corrected] area revealed a singular temporal pattern with hypoxic bottom waters in winter and oxygen-rich waters appearing in summer related with the availability of light and predominant microbes. Thus, oxygen consumption/production is likely to be regulated by the amount of light reaching the bottom, stimulating the production of oxygen by oxygenic phototrophs.