Limited monitoring activities to assess data on heavy metal (HM) concentration contribute to worldwide concern for the environmental quality and the degree of toxicants in areas where there are elevated metals concentrations. Hence, this study used in-situ physicochemical parameters to the limited data on HM concentration in SW and GW. The site of the study was Marinduque Island Province in the Philippines, which experienced two mining disasters. Prediction model results showed that the SW models during the dry and wet seasons recorded a mean squared error (MSE) ranging from 6 × 10 to 0.070276. The GW models recorded a range from 5 × 10 to 0.045373, all of which were approaching the ideal MSE value of 0. Kling-Gupta efficiency values of developed models were all greater than 0.95. The developed neural network-particle swarm optimization (NN-PSO) models for SW and GW were compared to linear and support vector machine (SVM) models and previously published deterministic and artificial intelligence (AI) models. The findings indicated that the developed NN-PSO models are superior to the developed linear and SVM models, up to 1.60 and 1.40 times greater than the best model observed created by linear and SVM models for SW and GW, respectively. The developed models were also on par with previously published deterministic and AI-based models considering their prediction capability. Sensitivity analysis using Olden's connection weights approach showed that pH influenced the concentration of HM significantly. Established on the research findings, it can be stated that the NN-PSO is an effective and practical approach in the prediction of HM concentration in water resources that contributes a solution to the limited HM concentration monitored data.