The white-clawed crayfish (Austropotamobius pallipes complex) is a crucial species complex in European freshwater ecosystems, but its population has faced severe declines since the 1860s due to pollution, habitat loss and fragmentation. The introduction of invasive crayfish species that carry the crayfish plague (Aphanomyces astaci), a water mold, has exacerbated this decline. The Avigliana Lakes Nature Park in Piedmont, Italy, which encompasses the Great Lake, Small Lake and Mareschi wetland, has been designated a Natura 2000 site supporting A. pallipes, particularly in the tributaries of the Small Lake. The aim of this study was to assess both the presence and distribution of A. pallipes in the study area and the physicochemical and ecological characteristics of its habitats. We also evaluated the proximity of invasive crayfish Procambarus clarkii populations to A. pallipes to further current understanding of potential health impacts and support management efforts. Macroinvertebrate monitoring was used to gauge overall ecosystem health and habitat suitability for A. pallipes. The results showed that A. pallipes was present at only two out of the six monitored sites, with no visible signs of disease. Macroinvertebrate monitoring indicated good water quality, while significant differences in pH, conductivity, and nutrient levels were found. Canonical correspondence analysis highlighted key environmental factors for A. pallipes, including conductivity, total dissolved solids, and vegetation. The lack of evidence for crayfish plague within the P. clarkii population may enable more effective management strategies and reduce potential health risks to the A. pallipes population. This study emphasises the need for ongoing monitoring and targeted management to mitigate invasive species’ impacts and conserve native crayfish populations.