Water and water habitats are essential to life and to the wellness of the communities that rely on them, as the Danube river is subject to human impact and vice versa, periodic surveys are required to determine the status of its pollution levels. In this work we used known microbiological indicators as well as physico-chemical ones to assess the ecotoxicological status of the Danube river from eleven locations partially forming the “Romanian–Bulgarian Danube Sector”. Most of the microbial communities found, and their densities, could be explained by point and diffuse sources scattered along the sector such as discharged household and farm wastewater, as well as nearby agricultural areas where fertilizers have been used and then leaked in the water stream during rainfalls. However, microbial data on non-point sources that lead to diffuse pollution of surface waters could be linked to such parameters and furthermore shown a slight correlation with the current status of fish communities.