The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulted in ecological changes of aquatic ecosystems, affected the aquatic food supply chain, and disrupted the socio-economy of global populations. Due to reduced human activities during the pandemic, the aquatic environment was reported to improve its water quality, wild fishery stocks, and biodiversity. However, the sudden surge of plastics and biomedical wastes during the COVID-19 pandemic masked the positive impacts and increased the risks of aquatic pollution, especially microplastics, pharmaceuticals, and disinfectants. The transmission of SARS-CoV-2 from wastewater treatment plants to natural water bodies could have serious impacts on the environment and human health, especially in developing countries with poor waste treatment facilities. The presence and persistence of SARS-CoV-2 in human excreta, wastewaters, and sludge and its transmission to aquatic ecosystems could have negative impacts on fisheries and aquaculture industries, which have direct implications on food safety and security. COVID-19 pandemic-related environmental pollution showed a high risk to aquatic food security and human health. This paper reviews the impacts of COVID-19, both positive and negative, and assesses the causes and consequences of anthropogenic activities that can be managed through effective regulation and management of eco-resources for the revival of biodiversity, ecosystem health, and sustainable aquatic food production.