Abstract Waste stabilization pond (WSP) systems exist in many countries affected by climate change causing increasing demand for irrigation water. There is little long-term experience with WSP in Africa, and thus, this study provides a comprehensive investigation of a WSP in Namibia. One of its treatment trains was upgraded with mechanical and anaerobic pre-treatment, and post-treatment and compared to a second train without upgrades. The pre-treatment showed positive results on COD, TSS and partially pathogen removal. E. coli were reduced to the new EU reuse standard of 1,000 MPN/100 mL for fodder irrigation, P. aeruginosa stagnated and Enterococci levels increased. The main pathogen reduction happened during pre-treatment and in the baffled facultative pond. In contrast, the post-treatment only reduced 5% of algae-based chlorophyll-a. Among the top 20 genera, Pseudomonas was most dominant. With different upgrades, hygiene requirements especially for restricted fodder irrigation can be reached. At the same time, high total tCOD and TN effluent values did not meet different reuse standards. But as the tCOD mainly consists of algae, adding biomass and TN fertilizer to the barren soil, it raised the question if all parameters set in the standards are applicable for WSP or should be adapted to their specific purpose.