Soil waterlogging is an environmental limitation that is promoted by changes in rainfall patterns and negatively affects plant physiology, growth, and development, coffee production, and exports in Colombia. The objective of this research was to evaluate responses in growth, water status, and chlorophyll fluorescence parameters for plants under different waterlogging conditions. The evaluations were carried out on six-month-old “Cenicafé 1” variety seedlings that were suitable for establishment in the field. The seedlings were subjected to different waterlogging periods: 4, 8, 12, and 16 days, using a completely randomized block experiment design with 30 replicates. Total dry mass (TDM), total leaf area (TLA), and the total number of leaves (TNL) were performed, and growth indices were calculated. The leaf water potential (Ψpd and Ψmd), maximum efficiency of photosystem II-FV/Fm, and electron transport rate (ETR) were also measured. Waterlogging for 16 days caused a 57% reduction for TDM, which was significant starting at 4 days. Statistical differences in the TLA were detected after 12 days, with decreases of 29%. The Ψpd, Ψmd, Fv/Fm, and ETR were sensitive to waterlogging, which decreased noticeably after 8 days. The results indicated the physiological performance and growth of the coffee cv. “Cenicafé 1” plants were significantly affected by waterlogging conditions after eight days.