This study aimed to characterize the material composition responsible for clogging the porous medium of horizontal subsurface flow constructed wetland (HSSF-CW) systems, which is detrimental to a proper system operation. Six completely clogged HSSF-CWs were used after treatment of swine wastewater. Operating conditions of these systems were named CW-C (HSSF-CW 1 and HSSF-CW 4, non-cultivated, i.e. controls), CW-T (HSSF-CW 2 and HSSF-CW 5, cultivated with Tifton 85 (Cynodon spp.)), and CW-A (HSSF-CW 3 and HSSF-CW 6, cultivated with alligator weed (Alternanthera philoxeroides)). The results showed that most of the clogging material was composed of total fixed solids (95, 84, and 82% in CW-C, CW-T, and CW-A, respectively). However, total volatile solids (TVS) mostly affected pore clogging. The larger accumulations and productions of TVS in CWs might have originated from dead plants.