Silver nanomaterials are widely used in commercial products, because the released silver nanomaterials be worried about ecotoxicity of freshwater organisms in environment. We have focused on reducing nanotoxicity using environmentally-friendly biological process by hydra cells. The hydra has a strong regenerative capacity about toxic chemicals, excellent adhesion and aggregation of hydra cells through self-organization during hydra regeneration stages. The hydra regeneration test examined two types of silver nanocolloids (Ag NCs) and silver nanotubes (Ag NTs) at concentrations of 5, 10, 50, 100 mg/L, respectively. In addition, we compared to the antimicrobial effects against E. coli (Gram-negative) and S. aureus (Gram-positive) bacteria by Ag NCs, Ag NTs and the Ag NCs including hydra cells. The aim of this study is not only to investigate the reducing nanotoxic effects in bacteria by the mixed silver nanomaterials including hydra cells but also to compare the nanotoxicity between Ag NCs and Ag NTs. Our results suggest that the silver nanomaterials including hydra cells can be reduced to nanotoxic effects in both E. coli (Gram-negative) and S. aureus (Gram-positive) bacteria. Because, the mixed Ag NCs including hydra cell were coiled around Ag NCs, which may inhibited by Ag NCs aggregations and the blocked silver ions. Furthermore, the shapes of silver nanomaterials are different nanotoxic effects according to the species sensitivity between hydra and bacteria.