An algorithm of alignment calibration for Ultra Short Baseline (USBL) navigation systems was presented in the companion work (Part I). In this part (Part II) of the paper, this algorithm is tested on the sea trial data collected from USBL line surveys. In particular, the solutions to two practical problems referred to as heading deviation and cross-track error in the USBL line survey are presented. A field experiment running eight line surveys was conducted to collect USBL positioning data. The numerical results for the sea trial data demonstrated that the proposed algorithm could robustly and effectively estimate the alignment errors. Comparisons of the experimental result with the analytical prediction of roll misalignment estimation in Part I is drawn, showing good agreement. The experimental results also show that an inappropriate estimation of roll alignment error will significantly degrade the quality of estimations of heading and pitch alignment errors.