The weekly measurement of physico-chemical and biological parameters was done during the spring of 2008 in order to assess the level of eutrophication in the Kotor Bay. Chlorophyll a was used as trophic level indicator and its values varied from minimal 1.00 mg/cubic meter in June on the depth of 10 m to maximal 3.71 mg/cubic meter on the sea surface in May. According to Nixon criteria during investigation period it can be concluded that the area in question is oligotrophic. On the other hand, according to UNEP criteria which are somewhat stricter when the concentration of chlorophyll a is in question, Kotor Bay was mesoeutrophic area.

Zooplankton community analysis was conducted for spring (April - 07) and summer (August - 07) in Boka Kotorska Bay. Analyses included determination of biomass and qualitative composition. Data are given on the number of specimens per cubic meter as well as on the volume organisms. Qualitative composition showed domination Copepoda of zooplanktons groups.

This paper presents results of measuring the contents of certain bioindicators in samples of digestive gland and lung of mussels (Mytilus galloprovincialis). The results were obtained in the framework of the Program for monitoring ecological status in Montenegro from 2009 to 2011 year. Samples were collected from two locations: Kotor-Dobrota (wild mussels) and the site of Bijela (caged mussels). Dynamic of sampling was twice a year, in April and September. In order to estimate the spatial distribution and temporal trends of pollution the results were compared with analysis of biomarkers in the three localities in the Slovenian coastal waters (bays Piran, Koper and Strujan). Biomarker responses showed no differences between these positions in the southern and northern Adriatic.

Qualitative and quantitative phytoplankton analysis was determined using standard microscopic methods and high performance liquid chromatography (HPLC) in the Bay of Kotor, seasonally, from April 2008 to March 2009. Diatoms represents dominant group of microphytoplankton with maximum in spring period. Dinoflagellates reached maximum value in summer period, and followed by cyanobacteria bloom. Dominant biomarkers, fucoxanthin, alloxanthin, 19'-heksanoloksifukoxanthin, zeaxanthin and chlorophyll b, show a similar distribution as the appropriate phytoplankton assemblages during the researches in Kotor Bay.

Mediterranean mussels, Mytilus galloprovincialis, are recognized bioindicators used in investigation of genotoxic pollution in the areas under the impact of anthropogenic activities. In July and August 2011 specimens of M. galloprovincialis were collected from 5 sites of Boka Kotorska Bay, Montenegro. Level of DNA damage was measured in gills, haemolymph and digestive gland with alkaline comet assay. Significant increase in DNA damage was detected in tissues of mussels collected from polluted sites comparing with mussels collected from the clean reference site Dobrota. The highest response to pollution was found in gills and digestive gland cells.

Arsenic is very toxic element and great pollutants in the environment. In this work we determine the content of arsenic in sea water from different sampling points of Montenegrin coast (mouth of river Bojana, Valdanos, Bar port, earlier Bar, Platamuni, Tivat bay) in winter and spring period. The content of arsenic was determined by using hydride AAS technique (Perkin Elmer, model 3300). The results were compared with the literature data and standard reference materials (Sea water CASS-1 National Research Council Canada-NRCC).

Influence of eutrophication to the phytoplankton community were studied in the inner part of Boka Kotorska Bay (Kotor Bay and Risan Bay) from September 2003 to August 2004. Kotor Bay and Risan Bay is very interesting area because the influence of natural and anthropogenic eutrophication are mixed very often. Microphytoplankton density is high (greater than 10**6 cells/cubic dm) what is characteristic eutrophic area, to the highest eutrophic area (greater than 10**7 cells/cubic dm). These values we stated in the surface, because in this layer were the best conditions. In same time we stated very high values: SiO2, oxygen saturation and chlorophyll a. The conclusion is: Boka Kotorska Bay and especially Kotor Bay (as a part of Boka Kotorska) has to be protected of dangerous consequences such as blooming. It is needed to regulate wastewater, their purification and permanent control physico-chemical and biological parameters, and especially phytoplankton component.

Sea urchin, Paracentrotus lividus belongs to Echinoderms and has wide distribution as well in Meditarranean Sea as in the Adriatic Sea. It is very appreciated as object for testing negative impact of pollution, so can be used as bio indicator of sea water and sediments quality. Identification of the presence of this animal is done at 11 locations inside the Bay of Boka Kotorska (Montenegro), during 2005/2006. Obtained results show that the sea-urchin inhabit only outer part of Boka Kotorska Bay, where is open sea impact very strong, while inner part of the Bay is characterized by absence of Paracentrotus lividus, what can be caused by potential low quality of the sea water in the Bay.

There are just a few data about species and quantities of phytobenthos for the Montenegrin coast, so that us one of the difficulties for the monitoring of changes caused by human impact. With the aim to contribute to the better knowledge of phytobenthos in this area we described distribution of Cystoseira barbata in the inner part of the Boka Kotorska bay and state of the environment in this aquatory.