The papar deals with the possibility of different types of seas protection from ballast waters, starting with administrative measures up to the technologies proposals by which those waters could be treated. The problem of ballast waters in the Montenegrin part of Adriatic Sea is in focus in this paper, and the proposal for protection measures are elaborated.

Research of presence and distribution of algal ordo Cystoseira has been done in 8 locations of Montenegrin coast. Presence of 8 species is confirmed and analysis of their aggregation on locations and aggregation of locations based on physico-chemical parameters of sea water and exposition to the waves are studied. Possibility of using these organisms as bioindicators is suggested.

As other areas on Montenegrin coast, Bokakotorska bay is also under a heavy impact of anthropogenic factors and the activities on the shore. The aim of the present work was to determine the levels of lead and cadmium in coastal surface sea water and sediment at three stations located in the inner shore waters Boka Kotor bay, and at one station located off shore Montenegrian coast considered as a reference station. The comparison of the results obtained for the inner shore stations with reference station showed that the content of this metals in some station are considerable increased in ratio to reference station.

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.