Polishing ponds are natural systems used for the post-treatment of upflow anaerobic sludge blanket (UASB) effluents. They are designed as maturation ponds and their main goal is the removal of pathogens and nitrogen and an additional removal of residual organic matter from the UASB reactor. This study aimed to evaluate organic matter and suspended solids removal as well as sludge accumulation in two shallow polishing ponds in series treating sanitary effluent from a UASB reactor with a population equivalent of 200 inhabitants in Brazil, operating since 2002. For this evaluation, long-term monitoring of biochemical oxygen demand and total suspended solids and bathymetric surveys have been undertaken. The ponds showed an irregular distribution of total solids mass in the sludge layer of the two ponds, with mean accumulation values of 0.020 m3 person−1 year−1 and 0.004 m3 person−1 year−1 in Ponds 1 and 2, leading to around 40% and 8% of the liquid volume occupied by the sediments after 11 years of operation. The first pond showed better efficiency in relation to organic matter removal, although its contribution was limited, due to algal growth. No simple input–output mass balance of solids can be applied to the ponds due to algal growth in the liquid phase and sludge digestion in the sludge.