Mechanical harvesting is quick and effective way to remove nuisance macrophytes and improve recreational use and aesthetics in shallow lake. However, applying mechanical harvesting to macrophytes in eutrophic shallow lake with weak resilience and strong perturbation raises concerns of the public and scientific communities. A combination of field investigation and remote sensing was used to determine the potential driving factors of macrophyte degradation in a eutrophic shallow lake from 2014 to 2017, including a comparative analysis of preserved and harvested areas to determine the impacts of mechanical harvesting. Over 95% of macrophytes had disappeared by 2017 in both preserved and harvested areas, with no significant difference in macrophyte distribution area or decline rate between the two by that time. The decline rate in the harvested area (76.7%) was slightly higher than in the preserved area (61.7%) in 2016 after performing the mechanical harvesting in 2015. The results demonstrate that mechanical harvesting is not the definitive driving factor for macrophyte loss, but it could accelerate the decline process. Bottom light availability (Secchi disk depth to water level), which decreased from 0.70 to 0.29 in 2015 and from 0.70 to 0.21 in 2016, is more likely the driving factor, caused by extreme water level increase events in two consecutive years (2015 and 2016) and decreased water clarity. Maintaining water clarity and low water level is crucial for macrophyte restoration.