Phosphate rock occurrences in western Venezuela are well-known in Cretaceous sedimentary sequences, which are associated to the Caribbean-Tethyan passive margin, along an SW-trend belt of the Venezuelan Andes chain. In this study, the geochemical characteristics of the Navay phosphate deposit were investigated to discuss the ocean paleo-oceanographic conditions and diagenetic controls that prevailed during the deposit formation. The rare earth elements plus yttrium (REY) concentrations were determined and normalized with the Post-Archean Australian Shale (PAAS) values to generate the REY patterns. Our results reveal a typical seawater signature, except for the absence of a marked negative Ce* anomaly (Ce/Ce* = 0.76–1.00). The determined seawater REY patterns, along to the calculated ratios for (La/Sm)N = 0.78–1.00, and (La/Yb)N = 0.34–0.66, are similar to the modern oceanic water ratios. These data point to a lack of diagenetic alteration on the primary REY signatures, which corresponds with a terrigenous-free marine sediment source for the REY content present in the deposit. In brief: i) the slightly negative anomalies displayed by the Ce* and Eu*, accompanied by the Mn depletion, ii) a relative enrichment of some transition metal elements (V, Cr, and Cu), and iii) the low Mo/U ratios, are all of them considered as geochemical indicators of suboxic to anoxic conditions, which were predominated during the phosphogenetic processes of the deposit. Furthermore, our data reveals an economic potential of the phosphorites as a raw material to produce phosphoric acid (H3PO4) as well as a source of supply for rare earth elements, by means of: i) relative high grades of P2O5 (15.46–30.09 wt %), ii) low CaO/P2O5 ratios (1.22–1.28), iii) a lack of organic matter, chert or chalcedony, iv) a low content of Mg (0.07–0.22%), v) REE concentrations varying from 141.82 to 256.53 μg/g, with an average value of 208.14 μg/g; and vi) concentrations for toxic elements (i.e., V, Cr, Co, Ni, Cu, Zn, As, Sr, Pb, and U) below or at the acceptable levels, in comparison to commercial phosphorites worldwide.