Seventy-five thermophilic fungi capable of growing at 45 °C were isolated from sugarcane bagasse samples and cultivated under solid-state fermentation (SSF). Two isolates showing the highest xylanase and cellulase production were selected and identified as Aspergillus fumigatus 5S2 and Aspergillus sp. 1.6C. Water hyacinth (WH) and sugarcane bagasse (SCB) were evaluated as lignocellulosic supports and carbon sources for enzyme production under SSF. Eight culture conditions were evaluated to identify the most suitable condition for enzyme production. Results revealed that substrate recalcitrance was a major limiting factor for enzyme production and that thermochemical pretreatment significantly improved substrate utilization. The highest enzyme activities were achieved on pretreated WH (PWH) supplemented with NaNO₃ and mineral salts. A. fumigatus 5S2 reached 810 U/g dry matter (DM) for xylanase and 95 U/g DM for cellulase, whereas Aspergillus sp. 1.6C reached 649 U/g DM of xylanase and 33 U/g DM of cellulase under the corresponding optimal culture conditions. PWH was mixed with SCB to improve the physical properties of the SSF support, including aeration, porosity, and water retention. The highest enzyme production levels were obtained using 1:1 and 1:0.5 (w/w) mixtures of PWH and SCB for A. fumigatus 5S2 and Aspergillus sp. 1.6C, respectively. SSF column bioreactors packed with these mixtures produced similar enzyme titers at 30 °C and 40 °C, confirming the thermotolerant nature of both strains.