Stable, aqueous, red-to-near infrared emission is critical for the use of silicon nanoparticles (Si NPs) in biological fluorescence assays, but such Si NPs have been difficult to attain. We report a synthesis and surface modification strategy that protects Si NPs and preserves red photoluminescence (PL) in water for more than 6 mo. The Si NPs were synthesized via high temperature reaction, liberated from an oxide matrix, and functionalized via hydrosilylation to yield hydrophobic particles. The hydrophobic Si NPs were phase transferred to water using the surfactant cetyltrimethylammonium bromide (CTAB) with retention of red PL. CTAB apparently serves a double role in providing stable, aqueous, red-emitting Si NPs by (i) forming a hydrophobic barrier between the Si NPs and water and (ii) providing aqueous colloidal stability via the polar head group. We demonstrate preservation of the aqueous red emission of these Si NPs in biological media and examine the effects of pH on emission color.