Selenium nanoparticles (SeNPs) have recently attracted attention for their antimicrobial and anticancer activities. Nevertheless, their use remains limited due to stability issues. The objective of this study is to investigate the impact of different reaction conditions (including the reducing and stabilizing agents, as well as reaction temperature) on the water dispersion characteristics, stability, and biological activity of SeNPs. The particle characteristics were controlled using sodium borohydride as a strong reducing agent and ascorbic acid as a mild agent. The impact of different stabilizers, namely sodium oleate, quercetin, gelatine, poly(ethyleneimine), and poly(diallyldimethyl-ammonium chloride), was investigated on both particle stability and biological activity. Several destabilizing processes occurred, one of which was continuous reduction to the final Se(-II) oxidation state, which was observed in both synthetic approaches, with using sodium borohydride or ascorbic acid as reducing agents. Non-stabilized SeNP dispersions were stable for a maximum of two weeks, while most stabilized SeNP dispersions remained stable for at least two months, and some remained stable for as long as six months. The antibacterial activity had strong effects, particularly against Gram-positive bacteria, and simultaneously low cytotoxicity against mammalian cells. SeNPs exhibited significant antibacterial efficacy, particularly against Staphylococcus aureus, including methicillin-resistant Staphylococcus aureus strains, even at concentrations as low as 1 mg L-1. SeNPs synthesized utilizing sodium borohydride demonstrate minimal cytotoxicity (EC50 > 100 mg L-1). Interestingly, SeNPs reduced by ascorbic acid demonstrated higher cytotoxicity (EC50 6.8 mg L-1) against the NIH/3T3 cell line. This effect is likely due to the combined cytotoxic effect of SeNPs and ascorbic acid acting as a pro-oxidant at high concentrations.