The objective of this study was to evaluate photosynthetic performance based on gas exchange traits, chlorophyll a fluorescence, and leaf water potential (ΨL) in nine Hevea brasiliensis genotypes from the ECC-1 (Élite Caquetá Colombia) selection and the cultivar IAN 873 (control) in response to different climatic (semi-humid warm and humid warm climates), seasonal (dry and rainy periods), and hourly (3:00 to 18:00) variations that can generate stress in the early growth stage (two-year-old plants) in two large-scale clonal trials in the Colombian Amazon. The photosynthetic performance in 60% of the Colombian genotypes was slightly affected under the conditions with less water availability (dry period, semi-humid warm site, and between 9:00 and 15:00 h), as compared with IAN 873, whose affectation was moderate in terms of photosynthesis rates, but its water conservation strategy was strongly affected. The ECC 90, ECC 83, and ECC 73 genotypes had the best photosynthetic performance under conditions of greater water limitation, and ECC 35, and ECC 64 had a higher water status based on the leaf water potential, with intermediate photosynthetic performance. This germplasm has a high potential for selection in rubber tree breeding programs in future scenarios of climate change in the Colombian Amazon.