Modern aquaculture practices fundamentally need upgrades under two aspects: i. eco-sustainability and ii. high quality of productions. Crustaceans may be both subjects of aquaculture productions and dangerous parasites of fish, to be chemically controlled in production plants. Salmon aquaculture, under this point of view, exhibits several issues, because of the high impacts of parasitic copepods: seventeen species of Caligidae copepods represent possible threats for fish and the environment. The drugs used to fight salmon louse are quite toxic and inefficient. For this reason, periodic treatments are needed to assure sufficient growth and survival of salmons, but they produce damages to the benthic and planktonic communities neighbour to the cages, in particular to crustacean’s communities. In addition, various economically important decapod crustaceans may be damaged by the presence of pesticides, so producing also an economic loss to the fishery activities. In this chapter, the main issues related to the use of pesticides in salmon aquaculture practices are reported, and the results of a newer investigation on natural compounds derived from cyanobacteria are exposed, as a promising tool to obtain an eco-sustainable control of parasitic copepods, maximizing the health of salmons and avoiding damage to other economically or ecologically important crustaceans.