The productivity of rice (Oryza sativa L.) in Ethiopia is below the potential due to spatial and temporal soil fertility variability and sub-optimal fertilization. This on-farm study was conducted in 2019 and 2020 to determine yield-limiting nutrients, quantify yield gaps, and determine indigenous soil nutrient supply (ISNS) for lowland rice in Fogera floodplain of Northwest Ethiopia. The study comprised the following treatments; NPKSZnB, -N (PKSZnB), -P (NKSZnB), -K (NPSZnB), -S (NPKZnB), -Zn (NPKSB), -B (NPKSZn), and Zero fertilizer (F0). The treatments were arranged in a randomized complete block design considering farmers’ fields as replications. The results revealed that the growth and yield of rice were significantly affected by the -N and F0 treatments. However, the other nutrient omissions did not significantly influence the mentioned parameters. The highest (2299.5 kg ha−1) yield response was recorded from the -N treatment. However, very low and insignificant yield responses were recorded from the other nutrient omissions. The average agronomic N use efficiency was 16.7 kg kg−1, which indicated a high probability of yield response to the application of N fertilizer. The lowest (42.4%) ISNS was found for N, while the highest ISNS (>90%) were recorded for P, K, S, Zn, and B. The yield gaps due to the omission of N was 57.6%, while the yield gaps due to the omission of P, K, S, Zn, and B were very low. Therefore, N was found to be the most yield-limiting and most deficient nutrient for the lowland rice production in the study area.