This work concerns the case study of a Mediterranean Ramsar salt lake (Fuente de Piedra, southern Spain) that receives the treated wastewater of the local village treatment plant. The wastewater goes through a system of canals, water dams, and three semi-natural ponds that were built in 2005. This work aims to investigate the capacity of the system to assimilate the impact of wastewater effluents on Lake Fuente de Piedra. For this, four points were sampled on 27–29 April 2016, at the inlet and the outlet points of the first and the third semi-natural ponds, with three replicates each. Temperature, pH, and conductivity at the inlet were 19.62 °C, 7.99, and 3262.67 μS/cm, respectively, and increased through the pond system by 7.59%, 8.04%, and 37.34%, respectively. Phytoplankton concentration indicators decreased from the inlet point to the outlet point (chlorophyll a from >500 to <20mg/L), as did the biovolume (from >5 × 1010 to 4.3 × 109 μm3/mL). Zooplankton biovolume, in contrast, increased three orders of magnitude from the inlet (3.5 × 107 μm3/mL) to the outlet point (1.6 × 109 μm3/mL). Heterotrophic bacteria (1.29 × 105 cfu/mL) and faecal enterococci (1033 ± 351 cfu/100 mL) were high at the inlet point, but decreased at the outlet point by almost three orders of magnitude. Total phosphorous and total nitrogen decreased 40.3% and 23.1% through the pond system. The results showed an improvement in water quality in its passage through the built system. Additionally, as permanent wetlands with acceptable water quality, the water system attracts wild fauna during the dry summer, leading to the conclusion that these semi-natural or artificial wetlands should be extrapolated to other aquatic ecosystems (Mediterranean wetlands) that receive contributions of residual waters. Better functioning of the treatment plant is desirable to improve the conservation of the Ramsar and adjacent wetlands systems.