A system for identifying ponding water located on a field from image data is described. In an approach, an image of an agricultural field is analyzed using a classifier that has been trained based on the spectral bands of labeled image pixels to identify a probability for each pixel within the image that the pixel corresponds to water. A flow simulation is performed to determine regions of the field that are likely to pool water after rainfall based on precipitation data, elevation data, and soil property data of the field. A graph of vertices representing the pixels and edges representing connections between neighboring pixels is generated. The probability of each pixel within the graph being ponding water is set based on the probability pixel being water, the likelihood that water will pool in the area represented by the pixel, the probability of neighboring pixels being ponding water, and a cropland mask that identifies which pixels correspond to cropland. A class for each pixel is then determined that maximizes the joint probability over the graph.