Fishing and aquaculture have an effect on aqueous medium where these activities are performed, which is the case in many other activities. Negative environmental pressures appear with the industrialization in each production branch. Although the spread of the fishery industry and the fast growth in aquaculture activities have brought important socio-economic benefits, they have also caused important ecological changes, and the negative effects of aquatic ecosystems on water quality and ecologic structure cause that various concerns are mentioned about the environment. The changes in water quality, eutrophication, algae explosions, the increase in the amount of phosphor, the decrease in dissolved oxygen amount, the changes in benthic fauna, the colonization in filament bacteria, the precipitation of solid matters, the increase in TSS, turbidity, the change in the color of the water, smell, disruption in the area use or changes in biological variety are some of the environmental pressures caused by fishing industry and aquaculture activities. When these effects are considered, it is easily understood that the fishery and aquaculture activities in aquatic media may damage the conformity of the water sources for drinking and usage, they may even cause that these sources disappear completely. In order to sustain water sources and aquaculture activities, the factors that might affect the water quality and aquatic ecosystem must be kept under control both before and during these activities; and it is also clear that protection and monitoring programs in aquatic systems are necessary and wise planning and management strategies must be prepared for these purposes.