Understanding wetland water quality dynamics and associated influencing factors is important to assess the numerous ecosystem services they provide. We present a combined self-organizing map (SOM) and linear mixed-effects model (LMEM) to relate water quality variation of multipond systems (MPSs, a common type of non-floodplain wetlands in agricultural regions of southern China) to their extrinsic and intrinsic influences for the first time. Across the 6 test MPSs with environmental gradients, ammonium nitrogen (NH4+-N), total nitrogen (TN), and total phosphate (TP) almost always exceeded the surface water quality standard (2.0, 2.0, and 0.4mg/L, respectively) in the up- and midstream ponds, while chlorophyll-a (Chl-a) exhibited hypertrophic state (≥28μg/L) in the midstream ponds during the wet season. Synergistic influences explained 69±12% and 73±10% of the water quality variations in the wet and dry season, respectively. The adverse, extrinsic influences were generally 1.4, 6.9, 3.2, and 4.3 times of the beneficial, intrinsic influences for NH4+-N, nitrate nitrogen (NO3--N), TP, and potassium permanganate index (CODMn), respectively, although the influencing direction and degree of forest and water area proportion were spatiotemporally unstable. While CODMn was primarily linked with rural residential areas in the midstream, higher TN and TP concentrations in the up- and midstream were associated with agricultural land, and NH4+-N reflected a small but non-negligible source of free-range poultry feeding. Pond surface sediments exhibited consistent, adverse effects with amplifications during rainfall, while macrophyte biomass can reflect the biological uptake of CODMn and Chl-a, especially in the mid- and downstream during the wet season. Our study advances nonpoint source pollution (NPSP) research for small water bodies, explores nutrient "source-sink" dynamics, and provides a timely guide for rural planning and pond management. The modelling procedures and analytical results can inform refined assessment of similar NFWs elsewhere, where restoration efforts are required.