Invertebrates in drinking water not only affect human health, but also provide migration and shelter for pathogenic microorganisms. Their residues and metabolites also produce DBPs (disinfection by-products), which have adverse effects on the health of residents. In this study, the contributions of the rotifers and nematodes to the BDOC (biodegradable dissolved organic carbon), BRP (bacterial regrowth potential) and DBPs in drinking water were explored, and the sheltering effects of chlorine-resistant invertebrates on indigenous bacteria and pathogenic bacteria were studied, and the health and safety risk of invertebrates in drinking water was also assessed. The contributions of rotifer BAPs (biomass-associated products), UAPs (utilization-associated products) of rotifer, and nematode BAPs to the BRP were 46, 1240, and 24 CFU/mL. Nematodes were found to have a sheltering effect on indigenous bacteria and pathogenic bacteria, allowing them to resist chlorine disinfection and UV (ultraviolet) disinfection. When subjected to a UV dose of 40 mJ/cm2, the inactivation rates of indigenous bacteria and three pathogenic bacteria decreased by 85% and 39–50% when bacteria were sheltered by the living nematodes; while decreased by 66% and 15–41% when they were sheltered by nematode residue. The safety risk posed by invertebrates in the drinking water was mainly due to their ability to promote bacterial regeneration and carry bacteria. This study aims to provide a theoretical basis and technical support for the risk control of invertebrates' pollution, and provides references for ensuring the safety of drinking water and formulating standards for the levels of invertebrates in drinking water.