Accurate prediction of spatial variation in water quality in small microwaters remains a challenging task due to the complexity and inherent limitations of the optical properties of small microwaters. In this paper, based on unmanned aerial vehicles (UAV) multispectral images and a small amount of measured water quality data, the performance of seven intelligent algorithm-optimized SVR models in predicting the concentration of chlorophyll (Chla), total phosphorus (TP), ammonia nitrogen (NH3-N), and turbidity (TUB) in small and micro water bodies were compared and analyzed. The results show that the Gray Wolf optimized SVR model (GWO-SVR) has the highest comprehensive performance, with R2 of 0.915, 0.827, 0.838, and 0.800, respectively. In addition, even when dealing with limited training samples and different data in different periods, the GWO-SVR model also shows remarkable stability and portability. Finally, according to the forecast results, the influencing factors of water pollution were discussed. This method has practical significance in improving the intelligence level of small and micro water body monitoring.