Wetlands are buffers for terrestrial runoff with the essential service of water purification. Despite its importance, they are experiencing degradation due to the combined effect of climate change and poor land-use practices. Studies of natural wetlands in Paraguay are scarce. We assessed wetland water quality conditions using pH, turbidity, total phosphorus (TP), and bacterial indicators of 12 natural wetlands located in protected areas (PW) or in the border of agricultural lands (AW) in the Paraguayan side of the watershed of Parana River. AW presented acidic pH values (x̄=5.5). We registered higher TP values in AW (x̄=0.14 mg/L) compared to PW (x̄=0.06 mg/L). For turbidity AW presented higher and variable values (x̄=425 NTU) than PW (x̄=34 NTU). In connected wetlands as the nutrient flows through the wetlands system to the reservoir concentration decreased 70% (0.1 to 0.03 mg/L) and the turbidity decreased from 112 to 42,6 NTU. This study observed a high degree of variability of bacterial indicators in water and sediment. The counts of coliforms in water and sediment samples were in the order E.Coli>Total coliforms>Fecal Coliforms. Long term contamination by organophosphorus and carbamate pesticides was pointed by the positive results in 100% of the sediment samples. As far as we can conclude wetlands has a key function in ecosystem function, health and preserving the water quality that enters to the reservoir, and protected PW presented better water quality conditions in terms of TP, turbidity, and bacterial indicators.