In this paper some results of investigations of physical, chemical and biological parameters were presented from the parts of Montenegrin coastal sea exposed to the impact of the open waters of the Southern Adriatic sea. As Herceg Novi area is simultaneously the part of the Boka Kotorska Bay (which goes deeply to mainland), eutrophication is more visiable there. Biological parameters were the most visiable indicators of eutrophication during these investigations.

On the base of monitoring of water quality for aquaculture, performed since 2010, it is noticed that two positions are showing increased level of trophicity and bacteriological contamination. Changes in sanitary quality of farms are especially intensive during the summer months, so the results of basic physical, chamical and biological parameters, measured during periods June-September 2010 and 2011 are presented and compared.

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.

Monitoring of ecological condition of the coastal sea of Montenegro has been carried out extensively since 1963 along with foundation of the Institute of marine Biology in Kotor (Montenegro). Recently, in accordance with recommendations of the Barcelona Convention, the LBS Protocol, the EU Framework Directive for coastal waters and domestic laws, in recent years has been carried out continuous monitoring of quality water, sediments, biota as well as ecological effects of pollution on constant monitoring positions in this southeastern part of the Adriatic. In this paper was given an over view of activities and the plan of long-term continuous monitoring of environmental quality and ecological condition of the coastal sea of Montenegro.

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.

New locations for the distribution of algae C. corniculata (Phaeophyceae) are presented, with a scope to improve scarce knowledge on phytobenthos of the Montenegrian coast. In the Bay of Boka Kotorska this algae is found on 10 locations and on 3 locations, on depth of 3 m and 5 m, measurements of wet weight and length of primary branches are done. Differences between biomass of algae are note between different depths and different seasons, but between different locations there are no significant differences.

In the beginning of 2008, on the Montenegrin coast is confirmed finding of new species, what was unknown until now in this part of Adriatic sea. The Sphoeroides cutaneus is tropical species with habitat in warm sea around Japan, China and Indonesia. Probably is one of the Lessepsian migrant. It tooks around 130 years for a fish to come through Suez Canal and Red Sea to Mediterranean, then through Otrant Strait into Adriatic sea. It is possible, also that this apparition has something with the global climate change and temperature rise in saltwater in Mediterranean as well as in Adriatic.

During the first five months of 2007 at one station in front of the entrace the Bay of Boka Kotorska, it was collected mesozooplankton using Nansen net, mesh netting of 200 microns. 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 zooplankton groups.

Utilization of open-sea industrial fishing techniques in catching small pelagic fish is still undeveloped at Montenegrin coast. Sardines and anchovies, are caught almost exclusively in the coastal area. In Bokakotorska Bay for the least several centuries exists a traditional type of fishery of small pelagic fishes by use of beach seines and artificial light. The Law on Marine Fishery states that the smallest allowed mesh size for catching small pelagic fish is 10 mm, but the fishermen use the mesh openings of 4.5-8 mm diameter as they exclusively collect immature individuals.

Monitoring of demersal resources in the Montenegrin coast start at 1997. We used commercial trawl vessels by monthly dynamic trawling. Processed total catch, estimated percentage part in total catch and CPUE (Catch per Unit Effort). We used standard fishery biology methods, estimation of population dynamic parameters, economical important fish, Red Pandora, Pagellus erythrinus, Red Mullet, Mullus barbatus, and crustaceans species, Pink shrimp, Parapenaeus longirostris. Also, we estimated relative and absolute biomass and MSY (Maximum Sustainable Yield) of this important demersal resources. This data give support to Ministry of Agriculture, Forestry and Water Management (of the Republic of Montenegro) to organize responsible exploitation of this resources. We finded center of higher biomass and relation to hydrographic factors, influence of income freshwater in the sea and increase of trophic level in this areas.