Nitrate pollution is a global environmental problem, and mean nitrate levels have risen by an estimated 36% in global waterways since 1990. Tracing nitrate sources is important for water quality management, and nitrate isotopes (δ15N-NO3− and δ18O-NO3−) are commonly used for this purpose because of the different isotopic compositions of different sources. However, the impact of nitrate sorption on matrix and desorption from matrix on N and O isotopic composition of nitrate in liquid phase has not been well clarified. To explore the mechanism for the changes in nitrate concentration and isotopes in liquid phase during sorption and desorption, this study took a shale sample (enriched in clay minerals and commonly exposed in the Earth), conducted a series of laboratory experiments for nitrate sorption and desorption, and studied the impact of sorption and desorption on nitrate N and O isotopic composition in liquid phase. The results showed that the shale sample exhibited a rapid sorption and desorption rate for nitrate in the surface water samples, with the nitrate concentration in the solution decreasing from 14.3 mg/L to 4.1 mg/L within 5 min. The sorption data fit the Langmuir model better than that of the Freundlich model. The maximum possible sorption (Qmax) for the shale sample was estimated to be 46 μg/g. Preliminary laboratory experiments showed that changes in δ15N-NO3− values were not obvious, and changes in δ18O-NO3− values in liquid phase were minor during sorption and desorption of the shale sample, suggesting that nitrogen isotopic fractionation can be neglected, and the sorption of nitrate by the shale sample has a very limited impact on the distribution of nitrate isotopes in liquid phase. However, the impact of nitrate desorption on the nitrate isotopes in liquid phase depends on the isotopic composition of exchangeable nitrate in the solid phase, which may be related to antecedent water–rock interactions. This study provides important information for elucidating the evolution mechanism of nitrate and its isotopic compositions following sorption-desorption, and is conducive to revealing the nitrogen cycle law in the environment.