The acid digestion method for extracting diatoms has been widely used to confirm death by drowning, but its reliability is still disputed because some diatoms can be destroyed during the extraction process due to treatment with strong acid and heat. There is a need to develop an efficient and reliable digestive method to overcome the limitation of the present analytical procedure. In this study, the reliability and efficacy of quantitative and qualitative diatom analysis from seawater by an enzymatic digestion method was evaluated. We confirmed the merit of the enzymatic method that used proteinase K instead of nitric acid in the conventional method. As a result, the enzymatic method showed a higher recovery ratio and better preservation of the diatom structure, which is essential for quantitative (diatom density) and qualitative (species) interpretation of diatom analysis. This result indicates that the enzymatic method can replace the conventional acid digestion method to confirm cases of death by drowning since it is more reliable and yields conclusive results.