Temporal characterization of physicochemical and bacteriological parameters of the Monastir bay was conducted out on 12 stations, during six sampling periods in 2014. Results showed a seasonal variation on the physicochemical parameters of the water masses (temperature, salinity, oxygen, pH, and turbidity) and well-oxygenated waters. Results indicated the absence of mineral phosphorus and the presence of low concentration of organic phosphorus in the stations close the coastline. Mineral nitrogen represented completely by nitrate, and organic nitrogen was detected everywhere during all sampling periods without any particular distribution. Chlorophyll-a concentrations present at low ratio characterizing an oligotrophic ecosystem showed two peaks, one during spring (April, May) and second in fall (September), and were significantly correlated with temperature (R2 = 0.82). Statistical analysis of different physicochemical parameters showed a correlation between temperature pH and oxygen. ANOVA tests showed a significant difference inter-sampling periods and between stations. Bacterial flora is dominated by halotolerant germs, which showed higher concentrations in the southern part of the studied area and are inversely correlated with salinity, turbidity, oxygen, and organic nitrogen (respectively R2 = − 0.62; − 0.79; − 0.84; − 0.72). The same evolution pattern was observed in mesophilic non-halo-obligate microflora. The Vibrionaceae concentration was correlated with water temperature and was within the standards for marine waters. Fecal coliform bacteria are absent in the studied area during all sampling periods. No particularity in water quality was noticed in this ecosystem, which characterized a good state. However, one can say that the collected data on physicochemical and bacteriological evolution can provide baseline information for assisting management of the Monastir bay, which represented a typical and important model of south Mediterranean Sea.