The rapid increase in the number of swine has caused pronounced environmental impacts worldwide, especially on water resources. As an aggregate, smallholdings have an important role in South American pork production, contributing to the net diffusion of pollution. Thus, duckweed ponds have been successfully used for swine waste polishing, mainly for nutrient removal. Few studies have been carried out to assess organic matter degradation in duckweed ponds. Hence, the present study evaluated the efficiency of two full-scale duckweed ponds for organic matter reduction of swine waste on small pig farms. Duckweed ponds, in series, received the effluent after an anaerobic biodigester and storage pond, with a flow rate of 1 m3 day−1. After 1 year of monitoring, an improvement in effluent quality was observed, with a reduction in biochemical oxygen demand (BOD) and total chemical oxygen demand (tCOD), respectively, of 94.8 and 96.7%, operating at a loading rate of approximately 27 kgBOD ha−1 day−1 and 131 kgCOD ha−1 day−1. Algae inhibition due to duckweed coverage was strongly observed in the pond effluent, where chlorophyll a and turbidity remained below 25 μg L−1 and 10 NTU. Using the study conditions described herein, duckweed ponds were shown to be a suitable technology for swine waste treatment, contributing to the environmental sustainability of rural areas.