Greenhouse gas (GHGs) emissions from freshwater ecosystems are a major component of global terrestrial landscape budgets. Currently, global warming is affecting these ecosystems and may trigger an increase in GHGs emissions, which may further enhance global warming. The identification and accurate quantification of aquatic ecosystems as sinks/sources of GHGs are vital for evaluating GHGs budgets and assessing possible climate feedback effects in order to improve climate models. In recent years, fluxes of carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O) have been observed from freshwater aquatic environments such as natural lakes, hydropower reservoirs, rivers, ponds, and drainage ditches. This review analyzes and summarizes research developments in GHGs emission paths, observation methods, and key factors affecting emissions from freshwater ecosystems. The mechanism of greenhouse gas production is a complex and interactive process that includes biochemical processes. The main emission paths from aquatic environments are diffusive fluxes across the air-water interface, bubble (ebullition) fluxes resulting from supersaturation of sediment, and plant-mediated fluxes. Attention has been recently been drawn to other emission pathways that contribute to total gas emissions at reservoir surfaces (e.g., gas release immediately below turbines and emissions further downstream in rivers). The monitoring methods vary for aquatic ecosystem emission pathways. Bubble fluxes are measured by funnel techniques, open dynamic floating methods, and ultrasonic detection technologies. Diffusive fluxes are measured by static chamber techniques, model estimations, micrometeorology, and tunable diode laser absorption spectroscopy (TDLAS). GHGs emission is conventionally measured using closed chamber to trap plant-mediated flux components. In addition, we discuss the impacts of physical, biological, hydrodynamic, and anthropogenic factors on GHGs emissions from aquatic ecosystems. We point out that an urgent and key direction for the future is to standardize the observation methods for GHGs fluxes from freshwater aquatic ecosystems and to consider temporal and spatial variability, which rely on long-term field observation.