The current work focused on the water quality of the Bega and Timis rivers measured by two methods. One of them is the method by which the water was analyzed from a physical-chemical point of view, and the other aimed at quantifying the degree of water pollution by biological methods. In this sense, diatoms were used. In the study, samples of water and diatoms were taken using specific techniques from the Bega and Timis rivers, starting from near the area of their formation until near the border with Serbia. Four sampling points were chosen on the Timis River plus one sampling point on the Surgani River, which is a tributary of the Timis, and six sampling points on the Bega River. The points were chosen specifically, being located downstream of the major sources of pollution. In order to locate the points, information was collected from the studies carried out as part of an extensive monitoring that spanned several years. The abundance and diversity of diatom species were used to calculate the Biological Diatom Index (BDI) and the Saprobity Index (SI). These two indices provide valuable information about organic or heavy metal pollution of water bodies.