This study was undertaken to investigate the effect of sea-cucumber (Holothuriaatra) population density on sea bottom sediment; redox potential, Total organic matter (TOM) assimilation, ammonification and nitrification activity. In protected aquaculture ponds at National Institute of Oceanography and Fisheries (NIOF), Four treatments of high population density (108 individuals/HPDP of 30m 2), mediumpopulation density (54 individuals/MPDP of 30m 2), low population density (18 individuals/LPDP of 30m 2) and reference (RP; Empty ofH.atra). Intestinal (Foregut and hindgut) of H. atra and ambient sediment samples were used. The data showed that presence of Holothuriaatra increase the Redox Potential of sediment and kept its characteristics in the oxidized form which enhanced the biological activities.The TOM decreased by16.04% (22.32% to 6.28%); 5.34% (10.54% to 5.2%); 3.02 % (8.02% to 5.0%) and 3.61% (8.35% to 4.74%) in HPDP, MPDP, LPDP and reference pond respectively. The maximum monthly mean of ammonia was 6.93µgg-1 in HPDP and the lowest mean was 0.09µg g-1 in recorded in LPDP. Ammonia and nitrate concentrations in the ponds of H. atrawereslightly reduced compared with the RP while nitrite concentration followed different pattern. The highest count of ammonifying,ammonium oxidizing and nitrite oxidizing bacteria were 1100 MPN/g, 460 MPN/g and64 MPN/g recorded in foregut contents.Meanwhile the lowest count was31.5 MPN/g, 20 MPN/g and 6.75 in RP, hindgut contents and LPDP respectively.The highest Ammonification and nitrification activity were36.69 µg/g/h and 1.19 µg/g/hrecorded in HPDP meanwhile, the lowest values were 7.38 µg/g/h and0.07 µg/g/h in RP. Ammonification rate and nitrification rate in foregut were higher than in hindgut contents and the ambient sediment. Data analysis showed ammonia-N; nitrate-N and nitrite-N concentration varied non significantly with H. atra population density (p˃0.05) while a highly significant effect recorded with oxidation reduction potential (Eh) and Nitrification activity (p<0.01) and significant effect on TOM matter and Ammonification rate (p<0.05). This study emphasizes the ecological role of the most dominant holothurians species, H. atra, especially in relation to organic matter assimilation, through its associated bacteria that enhance ammonification and nitrification processes in sediment.