The aim of this work is to assess and evaluate the energy and the membrane replacement cost for the seawater reverse osmosis (SWRO) plants. As a result of that, suggestions are given for energy cost reduction as well as optimum membrane cleaning procedure. A detailed comparative study was conducted for the energy recovery systems for SWRO plants available in the market. The energy consumption was measured in relation with other operating factors such as recovery, feed concentration, productivity, temperature, etc. All the data were collected from existing SWRO plants in different locations in Greece under real operating conditions. Four different energy recovery systems, which are used in seawater SWRO plants, were examined. These are the classical Pelton wheel, the turbocharger, the pressure exchanger and the Pelton wheel introduced by Grundfos company. The above energy recovery systems have been applied in small and medium size RO plants commissioned by different companies. The deterioration of the membrane performance is an actual fact leading after 2-5 years to the replacement of the membranes with a considerable cost. The lifetime of the membranes is greatly effected by the feed water quality and the pretreatment process. It was found that the normal cleaning procedure, which is recommended by the SWRO plant builders and the membrane makers, gives poor results especially for small size SWRO plants, with severe bio-fouling problems. As it is presented in this work, in some cases, destruction of the membrane modules is the result of severe bio-fouling. In this work data of the performance of the membranes before and after the cleaning procedure are presented and a different cleaning procedure is recommended. The later is based on the combination of hydrodynamic and chemical cleaning of the membranes, resulting in great improvement of the membranes performance. This cleaning procedure will extend the lifetime of the membranes and reduce the membrane replacement expenditures.