Dataset of the accompanying manuscript: H. Deguchi, C. Kashima, Y. Nakatani., Influence of Wave-dependent Parameterizations on Hydrodynamic and Water Quality Reproducibility in a Highly Enclosed Bay. #### data_obs #### Observed data are provided in three folders: 1) horizontal_distributions - Water quality observations conducted by the Research Institute of Environment, Agriculture, and Fisheries, Osaka Prefecture. 2) NOWPHAS - Wave observations conducted by the Nationwide Ocean Wave Information Network for Ports and Harbors (NOWPHAS). - Original data are available at https://www.pa.cgr.mlit.go.jp/suishitu/ 3) vertical_distributions - Water quality observations at three sites reffered to as OS, MT, and KB in the manuscript. - Original data are available at http://teiten.pa.kkr.mlit.go.jp/obweb/data/c0/c0_1.html