Wastewater may contain contaminants harmful to human health; hence, there is the need for treatment before discharge. Centralized wastewater treatment systems are the favored treatment options globally, but these are not necessarily superior in reduction of pathogens as compared to decentralized wastewater treatment systems (collectively called DEWATS). This study was therefore undertaken to assess the soil-transmitted helminth (STH) and Taenia sp. egg reduction efficiency of selected anaerobic baffled reactors and planted gravel filters compared to centralized wastewater treatment plants in South Africa and Lesotho. The risk of ascariasis with exposure to effluents from the centralized wastewater treatment plants was also assessed using the quantitative microbial risk assessment (QMRA) approach. Eggs of Ascaris spp., hookworm, Trichuris spp., Taenia spp., and Toxocara spp. were commonly detected in the untreated wastewater. The DEWATS plants removed between 95 and 100% of the STH and Taenia sp. eggs, with centralized plants removing between 67 and 100%. Helminth egg concentrations in the final effluents from the centralized wastewater treatment plants were consistently higher than those in the WHO recommended guideline (≤ 1 helminth egg/L) for agricultural use resulting in higher risk of ascariasis. Therefore, in conclusion, DEWATS plants may be more efficient in reducing the concentration of helminth eggs in wastewater, resulting in lower risks of STH infections upon exposure.