Wetlands are among the world's most productive ecosystems, providing crucial services including carbon sequestration, and greenhouse gases (GHG) mitigation. However, human pressures and warming increasingly threaten these ecosystems. Particularly, reduced water levels due to rising temperatures can lead to the emergence of organic matter stored in sediments, increasing decomposition and GHG emissions. Understanding wetland responses to environmental changes is important for effective management and conservation. This study investigated the effects of pond morphometry (area, depth, water volume), organic and inorganic nutrient inputs, and seasons on GHG fluxes (CH₄, CO₂, N₂O). Using hydrographic drones, gas-flow measurements, and C and N isotopic analysis, we assessed nutrient sources and GHG emissions in small freshwater wetlands within the Castelporziano Presidential Estate (Central Italy). We hypothesized that reduced morphometry increases GHG emissions, especially under high nutrient loading, due to rapid water warming and lower aquatic vegetation biomass. Ponds near cultivated fields were larger and showed elevated δ¹³C and δ¹⁵N, likely due to animal waste inputs, and elevated CH₄ emissions. Conversely, forest-surrounded ponds, being smaller and shallower, warmed faster and showed higher CO₂ fluxes. Overall, moist soil surrounding each pond emerged as hotspots for CH₄ and N₂O emissions, particularly during summer with high temperatures and low rainfall. CH₄ and CO₂ emissions increased with seasonal water temperature, peaking in July, while N₂O emissions were more substrate-specific and lacked consistent seasonal trends. Larger ponds had proportionally lower sediment volumes and displayed lower CO₂ emissions, suggesting their potential as carbon sinks. These findings highlight the importance of pond morphometry, land-use context, and seasonal dynamics in regulating wetland GHG fluxes. The progressive ponds’ drying due to global warming could increase GHG-emission, triggering a vicious cycle exacerbating climate change. This highlights the urgent need for management and conservation strategies to protect these ecosystems and their services in an ever-changing climate.