Aquaculture is the fastest growing food production industry. Due to the wrongly selected position of the fish farm and/or poor farming practices, fish farming may have different negative impacts on the environment at breeding site. One of the most common influence is environmental enrichment of the organic matter. This thesis deals with water and sediment sample from two locations in Mali Ston bay: cage fish production located in Kabli bay and a control station located in Mali Ston canal and two freshwater farms: carp fishery on the Ilova river and trout fishery on the Krka river. Methods that were used are: determination of particulate matter in water and sediment, x-ray diffraction analysis of sediments and determination of sediment carbonate content. The proportion of organic particulate matter in water at all study areas was higher during the summer months due to higher water temperatures, which may be related to a higher rate of feeding the fish, their faster metabolism and their greater activity. The results of this study showed that all three farms, in this case, did not show a negative impact on the amount of organic matter in water column and sediment. One of the most important factors are are nature of sediments, which are not prone to organic matter accumulation. In addition to the favorable composition of the sediment, good manufacturing practices can also have impact on the obtained result.