In this paper, we resolve the problem about calculation the key angle, estimate moisture interface reflection coefficient and eliminate abnormal data in situ measurement under complex conditions for the currently commercial underway water Hyperspectral Surface Acquisition Systems (SAS), and then examined the proposed method using the in situ data. The results showed that the underway-measured water-leaving radiance by SAS were quite consistent with these measured at fixed stations. Meanwhile, the variation trends of the underway-measured water-leaving radiance by SAS were similar as the underway water turbidities. These examining results indicate that the data processing method proposed is credible.The problems about calculation of the key angle, estimation of the reflection coefficient at the moisture interface, and elimination of abnormal data in situ measurement under complex conditions were solved for the currently commercial underway water Hyperspectral Surface Acquisition Systems (SAS). The proposed method was then examined using the in situ data. The results showed that the underway-measured water-leaving radiance by SAS were quite consistent with these measured data at fixed stations. Meanwhile, the variation trends of the underway-measured water-leaving radiance by SAS were similar as the underway water turbidities. These results indicate that the proposed method for the data processing is credible.