Creation of scientific basis for rational use of water resources is impossible without studying viability of the microorganisms, their influence on the formation of chemical properties of natural waters and an explanation of the principles of biochemical processes such as transformation of elements in the aquatic environment. The survey of microbial (bacterial) characteristics of watercourses in the Republic of Srpska was conducted on a total of 64 streams within Operational, International and National surveillance monitoring. Sampling and analysis of samples was performed during the period from May to October. The study included ecological and sanitary aspects of river quality.

Water quality monitoring of surface waters encompasses the watercourses of the river basins of Una, Vrbas, Bosna, Drina, Ukrina and the direct Sava basin. Apart from comprehensive analyses which demand determinations of physical - chemical characteristics, as well as the ihtiofauna composition, special emphasis is given to the analysis of the macrozoobenthos. As a part of all water ecosystems, benthic invertebrate serve as a reliable indicator of the quality and changes of the environment, due to a series of advantages in relation to other communities. Most of the aquatic habitats, especially flowing waters of good quality of water and benthic state, enable various of benthic invertebrates communities with moderate formation of species within the overall number of the present individual species. This kind of communities react to possible changes in the community composition (abundance and macroinvertebrata composition).

In the scope of complex water quality analysis of the Bocac reservoir, as well as rivers which flow into and out of the Bocac reservoir (Vrbas, Crna Rijeka) during the period from May to September 2008, the contents and the dynamics of the phyto and zooplankton were analyzed as biological parameters. The qualitative contents of the phytoplankton includes 5 divisions of total 27 taxa from 16 species; the tributaries contain 30 taxa from 19 genuses. The zooplankton (Rotatoria, Cladocera and Copepoda) contain 22 taxa from 16 genuses; the tributaries contain 32 taxa from 19 genuses with huge dominance of the Rotatoria species. By saprobiological analysis, species of oligo and beta mezosaprobiological character previal.

In the year 2010 ichthyological research on some Vrbas River tributeries located on wider area of Banjaluka city (Bosnia and Herzegovina) was carried out and the occurrence of 14 fish species was recorded. On the basis of the occurrence and abundance of fish species indicators as limnosaprobic parameter, water quality of the analyzed watercourses variated from oligosaprobic to beta mesosaprobic (I and II class of bonity) with saprobic index from 1.27 for Švrakava River to 1.81 for Vrbanja River. The obtained results indicate that water quality of this Vrbas River watershed was on satisfactory level for multiple purposes (in order to sustain ichthyofauna diversity and production and as potential protected areas and spawning zone for some endangered domestic fish species).

Researches of the Zelengora natural lakes during 2008 were performed in Orlovacko, Kotlanicko and the Lake Donje Bare. Water quality analysis of natural lakes of Zelengora were based on preliminary examination of basic physical and chemical parameters, as well as microbiological parameters. In the scope of biological examinations, phytoplankton, zooplankton and benthic fauna were determined. Due to the lack of data on biodiversity of examined natural lakes and whole area of National park Sutjeska results obtained in this research could only represent the first step toward further examinations, as well as the nature and biodiversity preservation in the Republic of Srpska.

During the period of 2004-2005 ichthyological research on natural waters of Bardaca wetland (Bosnia and Herzegovina) was carried out and the occurrence of 24 fish species was recorded. On the basis of the occurrence and abundance of fish species indicators as limnosaprobic parameter, water quality of the analyzed watercourses (rivers Matura and Brzaja) was found to be beta mesosaprobic (the 2nd class of bonity) with saprobic index 2.02 for Marura River and 2.03 for Brzaja River. The obtained results indicate that water quality of this part Bardaca wetland was on satisfactory level for multiple purposes (as a source of water for Bardaca fishpond and in order to sustain ichthyofauna diversity and production.

In the project Quality of Drinking Water of Banja Luka City, during 2007 the colony of zoobentos around the water factory is followed. The composition of colony is different in both season and horizontal profile. The quality of water in litoral area of river is much worse, because polluted water from ambiental settlement and that is indicated by major number of Tubificidae. During monitoring of the states there was a change of qualitative and quantitative composition of colony, also and the change of individual domination of taxons.

In the case that water quality data or even discharge data are missing, pollution loads were calculated as application of appropriate simulation models of pollution transport. Models can be in different levels complexity. Accuracy of the results depends on the accuracy of measurement data. In this study water quality of River Neretva (prediction of BOD pollution loads) is modeled in section from Mostar to Žitomislić using numerical model MIKE 11. Model is calibrated on the basis of available experimental data. Data of another time series are used for verification of last mentioned. The comparative analysis between measured and simulated data showed that MIKE-11 is able to predict sufficiently accurate BOD and DO loads at the catchment outlet.

During the summer 2009 physical, chemical, biochemical and bacteriological analyses of water of rivers Mušnica and Suški Potok were performed. Microbiological analysis point out that waters belong to the 2nd class by Kohl. The river Mušnica had slightly polluted water, and river Suški Potok had very slightly polluted water. According to the Regulation on Classification of Surface Waters in Republic of Srpska (Bosnia and Herzegivina) all the observed parameters belong to the first or second water quality class. Only the stream Suški Potok has chloride concentration that exceeds a third-class quality. On the basis of observed characteritics it can be concluded that Mušnica and Suški Potok have a satisfactory water quality.

Water quality analysis of Zelengora natural lakes, were included researches of Kotlanicko, Orlovacko and Lake Donje Bare. Apart from comprehensive analyses which demand determinations of physical-chemical characteristics, special emphasis is given to the analysis of the makrozoobenthos. As a part of all water ecosystems, benthic invertebrate serve as a reliable indicator of the quality and changes of the environment, due to a series of advantages in relation to other aquatic communities. Most of the aquatic environments of good quality of water and benthic state, enable various of benthic invertebrates communities with moderate formation of species within the overall number of the present individual species. This kind of communities react to possible changes in the community composition (abundance and macroinvertebrata composition).