Subsurface waters from both hemispheres converge in the Western Equatorial Pacific (WEP), some of which form the Equatorial Undercurrent (EUC) that influences equatorial Pacific productivity across the basin. Measurements of nitrogen (N) and oxygen (O) isotope ratios in nitrate (δ15NNO3 and δ18ONO3), the isotope ratios of dissolved inorganic carbon (δ13CDIC), and complementary biogeochemical tracers reveal that northern and southern WEP waters have distinct biogeochemical histories. Organic matter remineralization plays an important role in setting the nutrient characteristics on both sides of the WEP. However, remineralization in the northern WEP contributes a larger concentration of the nutrients, consistent with the older “age” of northern thermocline‐depth and intermediate‐depth waters. Remineralization introduces a relatively low δ15NNO3 to northern waters, suggesting the production of sinking organic matter by N2 fixation at the surface—consistent with the notion that N2 fixation is quantitatively important in the North Pacific. In contrast, remineralization contributes elevated δ15NNO3 to the southern WEP thermocline, which we hypothesize to derive from the vertical flux of high‐δ15N material at the southern edge of the equatorial upwelling. This signal potentially masks any imprint of N2 fixation from South Pacific waters. The observations further suggest that the intrusion of high δ15NNO3 and δ18ONO3 waters from the eastern margins is more prominent in the northern than southern WEP. Together, these north‐south differences enable the examination of the hemispheric inputs to the EUC, which appear to derive predominantly from southern hemisphere waters.