The past decade has seen the major development of fish-farming industry, particularly for salmon, in the semi-enclosed coastal marine environment, which are characterized by high nutrient inputs mostly in the form of high protein content food and juvenile to the fish farm, has created some negative impact on the coastal ecosystem and the environment. The heterotrophic microorganisms are the major agents in natural ecosystem to reduce environmental stress, although their activities are also limited by a large number of ambient ecological variables. Our purpose in writing this research book is to bring together concepts and data from different research experiments to provide a foundation, both for understanding the problems we face, and for finding ways to progress toward of an eco-friendly environment. Findings from experiments conducted during different seasons of the year for improvement of eutrophic bottom environments by adding bacteria have been discussed. Method to add bacteria to the system, their source, morphological and physiological characteristics has also been revealed. We hope this book will be an interesting, informative and inspiring resource toward that end.