The present application relates to an innovative and optimized method and system for maintaining water quality in water bodies such as excavated inland structures and floating structures with bottoms comprising flexible membranes, using a simplified economic filtration system and degreasing system that requires much smaller filtration equipment than conventional centralized filtration systems and provides for consumption of significantly lower amounts of energy. The method of the invention allows activating a chemical application system, mobile suctioning device, and/or degreasing system based on information regarding turbidity, the color of the bottom of the water body, and amount of greases on the surface water layer of the water body, to adjust the water quality parameters within their limits.