Access to safe drinking water is a recognized human right and a policy priority, reflected in the United Nations’ Sustainable Development Goals (SDGs). To monitor progress on SDG Target 6.1—safely managed drinking water services—many countries now incorporate Escherichia coli water quality testing into nationally representative household surveys, including UNICEF’s Multiple Indicator Cluster Surveys (MICS). The objective of this study was to evaluate multiple aspects of existing MICS water quality testing techniques. A low-cost filtration kit (~$60 compared to ~$1200 for the standard kit) was piloted during a water quality study in Southern Malawi. The low-cost filtration kit performed well with no breakage, leakage or stability issues reported. An existing MICS quality control measure was also assessed. Results support the current practice of using pre-tested locally purchased bottled water to undertake “blank” negative quality control testing. The current practice of having enumerators count E. coli colonies was investigated and was found to be acceptable and valid. To increase the storage capacity of the belt incubation method, a reduced (18- vs. 24-hour) incubation time was investigated. If the purpose is to classify results by risk categories, it would be advisable to incubate samples for the additional 6 hours if after 18 hours a count is observed of only 1 or 2 CFU/100 mL lower than the cut-off for the next highest risk category. Overall, results were encouraging and support the widespread use of the low-cost filtration kit, with potentially significant cost savings. However, we recommend further research to investigate and quantify the impacts of an abbreviated incubation time on water quality results.