The productivity of wheat in the Mediterranean region is under threat due to climate-change-related environmental factors, including fungal diseases that can negatively impact wheat yield and quality. Wheat phenotyping tools utilizing affordable, high-throughput plant phenotyping (HTPP) techniques, such as aerial and ground RGB images and quick canopy and leaf sensors, can aid in assessing crop status and selecting tolerant wheat varieties. This study focused on the impact of fungal diseases on wheat productivity in the Mediterranean region, considering the need for a precise selection of tolerant wheat varieties. This research examined the use of affordable HTPP methods, including imaging and active multispectral sensors, to aid in crop management for improved wheat health and to support commercial field phenotyping programs. This study evaluated 40 advanced lines of bread wheat (Triticum aestivum L.) at five locations across northern Spain, comparing fungicide-treated and untreated blocks under fungal disease pressure (Septoria, brown rust, and stripe rust observed). Measurements of leaf-level pigments and canopy vegetation indexes were taken using portable sensors, field cameras, and imaging sensors mounted on unmanned aerial vehicles (UAVs). Significant differences were observed in Dualex flavonoids and the nitrogen balance index (NBI) between treatments in some locations (p 2 = 0.61–0.7 and R2 = 0.45–0.55, respectively) compared to the aerial AgroCam GEO NDVI (R2 = 0.25–0.35 and R2 = 0.12–0.21, respectively). We suggest as a practical consideration the use of the GreenSeeker NDVI as more user-friendly and less affected by external environmental factors. This study emphasized the throughput benefits of RGB UAV HTPPs with the high similarity between ground and aerial results and highlighted the potential for HTPPs in supporting the selection of fungal-disease-resistant bread wheat varieties.
