<p><strong>Abstract.</strong> Nitrogen and water availability are two of staple environmental elements in agroecosystems that can substantially alter canopy structure and physiology then crop growth, yielding large impacts on ecosystem regulating/production provisions. However, to date, explicitly quantifying such impacts remains challenging partially due to lack of adequate methodology to capture spatial dimensions of ecosystem changes associated with nitrogen and water effects. A data assimilation, where close-range remote sensing measurements of vegetation indices derived from a hand-held instrument and an unmanned aerial vehicle (UAV) system are linked to leaf and canopy photosynthetic traits quantified at plot level by portable chamber systems, was applied to capture and interpret inter- and intra-field variations in gross primary productivity (GPP) in lowland rice grown under flooded condition (paddy rice, PD) subject to three available nutrient availability and under rainfed condition (RF) in East-Asian monsoon region, South Korea. Spatial variations (SVs) in both GPP and light use efficiency (LUE<sub>cabs</sub>) early in growing season were amplified by nitrogen addition, and such nutritional effects narrowed over time. Shift planting culture from flooded to rainfed conditions strengthened SVs in GPP and LUE<sub>cabs</sub>. Intervention of prolonged drought event at late growing season dramatically intensified their SVs that are supposed to seasonally decrease. Nevertheless, nitrogen addition effects on SV of LUE<sub>cabs</sub> at early growth stage made PD field exert greater SVs than RF field. SV of GPP across PD and RF rice were likely related to LAI development less to LUE<sub>cabs</sub> while, numerical analysis suggested that consider spatial variation and strength in LUE<sub>cabs</sub> for the same crop type tends to be vital for better evaluation in landscape/regional patterns of ecosystem photosynthetic productivity at critical phenology stages.</p>