This study analyzes the full-scale results of a three-year eutrophication control and management in the Orbetello lagoon. We examined the cause/effect relationship among the resuspension of top layer sediment in the water column (carried out by specifically designated boats), the labile organic matter present in the sediments (LOM), and the values of Chaetomorpha linum high density mats, which insist in the disturbed areas. LOM values resulted inversely associated to the frequency of sediment disturbance. LOM decrease, together with higher oxidation levels, triggered the reduction of nutrient release with an immediate effect on algal masses: the decay of the mat under layer prevailed on the growth of the mat over layer. Conversely, with a reduced frequency of disturbance, and the consequent increase of both the LOM as well as the anaerobic processes of the sediment which promote nutrient releases, the algal growth showed a time lag of several months, in which the nutrients uptake was likely intense. The stored nutrients were then used only some months later, when the environmental conditions became favorable for the surprisingly rapid and impressive development of the mats.