Fourteen high altitude (> 2,500 m amsl) small Waste Stabilisation Pond systems (WSPs) commissioned during the last 12 years in the State of Mexico in Mexico, were built to a common 3-stage design. Each system is comprised of 2 parallel series of bio-digesters, anaerobic and facultative ponds. All fourteen WSP systems produce poor quality effluents, and eight studied in more detail did not meet any of the national standards for discharge to rivers or the standards required for reuse. The under-performance of these WSPs is underlined by the anaerobic condition of the upper reaches of the Lerma river which receives the sewage from the towns served by these treatment plants. Preliminary surveillance diagnostics identified fundamental operational problems in all eight WSP systems located in the upper Lerma catchment. The results of an intensive secondary diagnostic performance evaluation on one system were used to identify the reasons for under-performance. Under-performance was caused by under-design, hydraulic short-circuiting, adverse environmental conditions and poor operation and maintenance. A strategy for improvement of design and operation to meet national standards is presented.