Benthic attached diatoms (BADs), a major primary producer in lotic stream and river ecosystems are micro-sized organisms and require a highly magnified microscopic technique in the observation work. Thus, it is often not easy to ensure accuracy and precision in both qualitative and quantitative analyses. This study proposed a new technique applicable to improve quality control of aquatic ecosystem monitoring and assessment using BADs. In order to meet the purpose of quality control, we developed a permanent mounting slide technique which can be used for both qualitative and quantitative analyses simultaneously. We designed specimens with the combination of grid on both cover and slide glasses and compared their efficiency. As a result of observation and counting of BADs, the slide glass designed with the color-lined grid showed the highest efficiency compared to other test conditions. We expect that the method developed in this study could be effectively used to analyze BADs and contributed to improve the quality control in aquatic ecosystem health monitoring and assessment.