The antibacterial activity of different seaweed species against five fish pathogens (A. hydrophila, V. parahaemolyticus, V. alginolyticus, V. damsela and Vibrio sp.) has been evaluated. The ethanolic extract of C. sinuosa (CSE1) and dichloromethane extract of C. officinalis (COM) exhibited the highest antibacterial activity with activity index (AI) = 1.4 ±0.74 and 1.2 ±0.71, respectively. When the extracts were encapsulated into calcium alginate beads their antibacterial activity against the most susceptible bacterial pathogens showed that the significant growth inhibition was against V. parahaemolyticus after 5 min post addition of the beads recording 1.4 and 2 fold decrease in the growth, respectively. Recycling of the (CA/COM) beads was carried out for 7 successive cycles with success in elimination of V. parahaemolyticus. The potential applications of encapsulated extracts for elimination of microbial load in fish rearing water and antifouling activity were proved in the current investigation. The chemical composition of the bioactive extracts (CSE1) and (COM) was determined using GC/MS analysis which revealed the presence of several constituents that have been reported to exhibit antimicrobial activity. Additionally, the dichloromethane extract (COM) produced six major components including n-nonadecane, 1,2,3propanetricarboxylic acid, 2-(acetyloxy)-, tributyl ester, 2-methylhexadecan-1-ol, 1-docosene, 1-eicosanol and chloroacetic acid, octadecyl ester. However, the ethanolic extract (CSE1) was characterized by the presence of fatty acids, fatty acids ethyl esters and aromatic hydrocarbon where the most abundant compound was n-tridecanoic acid ethyl ester.