Heat stress reduces photosynthetic capacity, quality, and yields causing significant economic loss. In most cropping systems, the lack of cultivars with more resilience to heat wave cycles put perennial crops such as walnut commercial production under severe threat. The available walnut cultivars are highly sensitive to higher temperatures causing significant annual loss and inducing long-term susceptibility to other stressors. Germplasm collections provide a diverse cultivar option and hold the potential for improving crop productivity under heat tolerance. Over a two-year study, we screened 11 Juglans regia accessions for physiological responses to heat stress and recovery potential in the USDA-ARS National Clonal Germplasm. Net assimilation rate (An) under heat and recovery in response to irrigation differed significantly among accessions; accessions 3 and 5 with inherently higher An exhibited greater An under 35° and 40°C before irrigation and were the only accessions to have the highest An under those temperatures after irrigation. Stomatal conductance (gs) declined under higher temperatures for most accessions, while leaflet water potential decreased in a few accessions under high temperatures. When a subset of accessions including two high-performer (A3 and A5) and two low-performer (A1 and A8) were monitored over two full heat waves, we found the high-performer ones to keep their An higher than A1 and A8 under both 35°C and 45°C even before irrigation. A5 exhibited the highest performance under 35°C after irrigation, similar to its performance at the baseline which was prior to heat wave cycles. Greater An in A3 and A5 was supported by higher maximum carboxylation rate, electron transport rate, maximum photosynthesis, and photosystem II efficiency, in line with their higher carbonic anhydrase activity. In conclusion, J. regia accessions with inherently higher An and gs showed greater tolerance and recovery in response to irrigation under natural heat stress, supported by their greater biochemical and enzymatic activities.