Biogenic nano-hydroxyapatite (bio-nHAP) has recently gained great interest in many domains, especially in the remediation of heavy metal-contaminated soil, due to its high reactivity, low cost, and eco-friendly nature. The co-transport and reaction of bio-nHAP with Pb(II) in saturated porous media, however, are not well understood. This work investigated the effects of ionic strength (IS), ionic composition (IC), dissolved organic matter (DOM), and flow velocity on transport-reaction dynamics of Pb(II) and bio-nHAP by combining column breakthrough experiments and model simulations. Results showed that the mobility of Pb(II) was significantly enhanced with increasing IS/IC but less affected by flow velocity during the transport-reaction process of bio-nHAP and Pb(II) in the saturated sand column; while the transport of bio-nHAP was restricted by increasing IS/IC but facilitated by increasing velocity. IC, IS, and velocity only slightly affected the reaction kinetics between Pb(II) and bio-nHAP, likely due to the fast reaction rate between Pb(II) and bio-nHAP and precipitation of pyromorphite. The transport dynamics of bio-nHAP and Pb(II) were significantly changed by DOM, and this effect depended strongly on the type of DOM with different molecular weights. Breakthrough curves of Pb(II) and bio-nHAP exhibited apparent “anomalous”, sub-diffusive transport behaviors, which could be well quantified by a novel tempered fractional derivative bimolecular reaction equation (T-FBRE). Our findings highlighted the accurate simulation of the co-transport and reaction of bio-nHAP with Pb(II) using T-FBRE and had a great benefit for risk assessment and remediation strategy development for Pb(II) contaminated soil.