This study addresses the lack of comparative research on algae/cyanobacteria elimination technologies in the existing literature. Our investigation focused on evaluating the performance of three commonly used algae/cyanobacteria removal processes: ultrasound (20.8 kHz), copper sulfate and biotic algicide (Bacillus subtilis). The evaluation considered both algae/cyanobacteria removal efficacy and the consequent changes in extracellular microcystins (MCs). To achieve this, we employed real eutrophic water as the test water. The ultrasound treatment demonstrated effective algae/cyanobacteria removal, with an average rate of algae/cyanobacteria decreasing (RAD) ranging from 0.50 to 0.99 µg chlorophyll a per liter per minute (µg chlorophyll a/L·min). On the other hand, the copper sulfate and biotic algicide treatments exhibited relatively lower rates of algae/cyanobacteria removal, with average RAD values of 0.21 to 0.38 µg chlorophyll a per liter per day (µg chlorophyll a/L·d) and 0.10 to 0.13 µg chlorophyll a per liter per day (µg chlorophyll a/L·d), respectively. Moreover, we observed significant increases in extracellular MCs in the ultrasound and copper sulfate treatments. The corresponding values of the increment of extracellular MCs accompanying removal per microgramme (µg) chlorophyll a (IEMARMC) were 0.34 to 2.43 µg MCs per µg chlorophyll a (µg MCs/µg chlorophyll a) and 18.13 to 185.08 µg MCs per µg chlorophyll a (µg MCs/µg chlorophyll a), respectively. However, in certain conditions where sufficient dosages (0.5 to 2 mg/L) and reaction time (≥8 days) are provided, the biotic algicide treatment could result in a decrease in MCs compared to an untreated control group (IEMARMC: −43.94 to −32.18 µg MCs per µg chlorophyll a). This suggests that the biotic algicide effectively degraded the MCs. In addition, we developed a one-dimensional MC diffusion model in still water based on Newton’s second law, which exhibits excellent simulation capabilities.