Various methods have been proposed for in situ measurement of nitrate concentrations from the ultraviolet (UV) absorbance spectrum of seawater with stable salinity and constituents. However, salinity and temperature affect the UV absorption spectrum of seawater. In sea areas with large variability in salinity and water temperature, accurate nitrate ion concentration measurements remain challenging. We performed in situ measurements of nitrate, chloride, and bromide in estuarine seawater with different salinity compositions and applied water temperature compensation. First, the impact of water temperature on the UV absorbance of chloride, bromide, and nitrate was experimentally investigated and represented in a mathematical model. Next, chloride, bromide, and nitrate concentrations were estimated by suppressing the impact of residual components from the UV absorbance spectra of seawater using principal component regression (PCR). Hence, the chloride, bromide, and nitrate concentrations were determined by measuring the UV absorbance spectrum of seawater alone, without measuring water temperature and electrical conductivity. The proposed method was more accurate (±1.39 μM below 100 μM and ±0.90 μM below 20 μM) than the conventional method (±2.35 μM below 100 μM and ±1.88 μM below 20 μM) and PCR without water temperature compensation (±3.67 μM). In a field study, an in situ UV spectrophotometer with water temperature compensation was used to measure depth profiles of nitrate concentrations in estuarine seawater. We successfully measured the depth profiles of low chloride and high nitrate concentrations in the surface layer as well as high chloride and low nitrate concentrations in the lower layer. The proposed method enables in situ measurements of nitrate concentrations in waters with either stable or highly variable salinity and composition. Unlike conventional chemical analysis, our method can describe detailed spatiotemporal variations in nitrate concentrations.