On-site domestic wastewater treatment (ODWT) systems are receiving renewed interest due to their simplicity of implementation, affordability and efficiency. The most widespread ODWT system is the sand filter with vertical drained flow (SFVDF). To optimise the design and maintenance of SFVDFs, it is important to be able to check the conformity of the installations, judge their treatment performance in service and estimate possible evolution and life expectancy. As yet, however, no methodology has been developed to perform these tasks. This paper proposes a new methodology for diagnosing SFVDF systems in service. The development of this methodology relies on the development of on-site characterisation of the filtering material based on the use of a light dynamic penetration test and image processing. From this, the paper proposes an automatic tool for detecting the presence of clogging in a filter and a methodology to estimate the hydraulic conductivity of the filtering material without destroying the filter. The global methodology for diagnosing SFVDF systems is presented and illustrated for a real case in order to demonstrate its advantages and efficiency.