Acanthamoeba castellanii plays a vital role in aquatic ecosystems by regulating microbial populations and participating in biogeochemical cycles. However, its overproliferation may disrupt ecological balance and pose public health risks, such as Acanthamoeba keratitis. This study explores the potential role of giant viruses (GVs) as natural regulators of A. castellanii populations in four freshwater lagoons (Daniel Álvarez Burneo, Jipiro, Carigán, and Punzara) in southern Ecuador. Using in vitro co-culture systems and phase-contrast time-lapse microscopy, we observed infection-associated phenomena, including cell rounding, detachment, and lysis, with notable variation among lagoons. Our results suggest that GVs are ubiquitous and can affect amoebic survival, acting as key modulators of population dynamics and contributing to ecosystem stability. In addition, the study highlights the biotechnological potential of GVs, particularly through the exploration of open reading frames (ORFs) and other genetic elements with applications in genetic editing, bioremediation, and pathogen control. The integration of microscopy with molecular approaches, including gene sequencing, is proposed as a necessary next step to a better understanding of GV-amoeba interactions and their broader ecological significance.