The unconformity-related uranium (URU) deposits, which are best developed in the Proterozoic Athabasca Basin (Canada), can be divided into the monometallic (U) and polymetallic (U-Ni-Co-As) subtypes. Different models have been proposed to explain the formation of the two subtypes of URU deposits. The conventional “diagenetic-hydrothermal” model suggests that both subtypes formed from oxidizing, acidic basinal brines in a unified mineralization system, whereas a newly proposed model suggests that the polymetallic deposits formed from monometallic U deposits superimposed by Ni-Co-As mineralization. While the second model has been the subject of ongoing debates, there are also unanswered questions in the diagenetic-hydrothermal model; in particular, it remains unclear what geological factors controlled the formation of one subtype or another in a unified mineralization system. This paper aims to address this question with geochemical modeling of hydrothermal U-Ni-Co-As transport and deposition using the Geochemist's Workbench (GWB) software. The conditions for U-Ni-Co-As transport were examined with thermodynamic modeling. The results indicate that highly oxidizing (log fO2(g) > −25), acidic (pH = 3.5) brines can transport large amounts (>100 ppm) of U together with Ni-Co-As, whereas moderately oxidizing (−40 < log fO2(g) < −25), less acidic (3.5 < pH < 6) brines can transport only minor amounts (<1 ppm) of U while still capable of carrying large amounts (>100 ppm) of Ni-Co-As, and very reducing (log fO2(g) < −40) brines with pH from 3.5 to 6 can dissolve only minor amounts (<1 ppm) of U and Ni-Co-As. The mechanisms of U-Ni-Co-As deposition were examined with reaction path modeling involving fluid-rock interaction and fluid-fluid mixing. The results indicate that as a U-Ni-Co-As-bearing, acidic, oxidizing brine progressively reacts with basement rocks or mixes with a reducing fluid, U precipitates before Ni-Co-As in relation to pH increase and fO2(g) decrease. In the case of fluid mixing, while U precipitation can be caused by any of the reducing agents (CH4(aq), H2(aq), H2S(aq), and Fe2+(aq)) in the reducing fluids examined, Ni-Co-As deposition requires the participation of CH4(aq) or H2(aq). Based on the modeling results, it is inferred that U and Ni-Co-As were not transported by the same fluid, otherwise all the URU deposits would be polymetallic. The U was most likely derived from the basin rather than from the basement, because as oxidizing basinal brines infiltrate and interact with basement rocks, their ability to dissolve and transport U quickly diminishes due to fO2(g) decrease and pH increase. In contrast, as these basinal brines infiltrate the upper part of the basement, which is moderately oxidizing, they retain the ability to dissolve and transport significant amounts of Ni-Co-As, enabling the scavenging of these metals from the basement. While all URU mineralization requires U-bearing basinal brines and reducing agents, the formation of polymetallic (U-Ni-Co-As) deposits depends on the availability of Ni-Co-As-rich lithologies in the upper part of the basement, together with an ample supply of robust reducing agents, such as CH4 and H2 that were derived from the deeper part of the basement. Therefore, although the possibility that polymetallic U-Ni-Co-As deposits formed from Ni-Co-As mineralization superimposing on monometallic U deposits cannot be ruled out, the results of this study demonstrate that both polymetallic and monometallic URU deposits can be formed in a unified diagenetic-hydrothermal mineralization system in the Athabasca Basin.