Inorganic fertilisers need to be applied only when the inherent soil fertility alone cannot supply the plant nutrient demand for rice. When managing such systems, identification of the most sensitive morphological and/or physiological characteristics of a rice plant and the growth stage at which those responses appear when soil phosphorus (P) and potassium (K) availabilities have declined are important. Such a practice will increase fertiliser-use efficiency and enhance environmental sustenance. Experiment was conducted in a field differing in initial soil P and K availabilities due to the application of four fertiliser treatments for three consecutive seasons. Observations in this experiment were made in the fourth season. Four fertiliser treatments were the application of (i) both P and K (P1K1), (ii) only P (P1K0), (iii) only K (P0K1), and (iv) no P and K (P0K0). Rice variety Bg300 was grown. Shoot samples were obtained at two-week intervals, while root and soil samples were collected using a soil core up to 80 cm depth at physiological maturity. At physiological maturity, root length, diameter, and root length density were not responsive to the declined soil P and K availability, whereas the total above-ground dry weight (DW) reduced in P- and K-deficient plots. Shoot physiological responses [i.e. reduced green leaf P and K concentrations, and increased phosphorus-use efficiency (PUE) and potassium-use efficiency (KUE)] were more prominent than shoot morphological responses (i.e. plant height, number of tillers, and total above-ground DW), throughout the growth cycle. The intensity (i.e. statistical significance) and duration of the appearance of K deficiency symptoms were lower than those of P. The most sensitive growth stage of rice to slight deficiencies of P and K was the tillering stage. This knowledge on the morphological and physiological shoot and root responses that can be observed during the lifecycle of a rice plant, and the growth stage(s) at which those responses are prominent in response to declining soil P and K availability can be used when identifying the development of soil P and K limitations hindering the optimal growth of rice plant, and sustaining rice cropping systems.