While there have been numerous studies on the rate and development of clogging in horizontal subsurface treatment wetlands (HSTWs) and, consequently, the effects on its hydraulic characteristics, research has not shown a clear understanding of the processes. The existing methods for measuring the impact of clogging provide limited information on the extension and degree of the phenomenon. This study aimed to evaluate the capacity of various measurement techniques to assess the degree and variation in space and time of clogging in HSTWs. Hydraulic conductivity at saturation (Ks) measurements were conducted using a newly implemented scheme, the drainage equation method, and traditional tracer tests, which were carried out in a full-scale HSTW system, located in Sicily, Italy, during 2019. After five years of operation, the results highlighted a severe decrease in Ks (<1000 m day−1) in the inlet zone (despite the fact that the filter gravel was replaced in 2017), a very high reduction of Ks along the central path inside the bed, a nonuniform flow through the HSTW, the presence of stagnant zones, and a reduction of the porosity of the bed gravel. Nonetheless, the mean values of the physical–chemical and bacteriological parameters at the hybrid treatment wetland (hybrid TW) outlet indicated that the partial clogging had no significant effect on the quality of the discharged water. Moreover, the results obtained using the different measurement techniques (in terms of both the Ks values and the flow distribution inside the bed) were consistent with each other and with results obtained previously for the same system. Finally, the most efficient combination of methods to assess clogging in HSTWs was identified.