The prediction of algal chlorophyll-a and water clarity in lentic ecosystems is a hot issue due to rapid deteriorations of drinking water quality and eutrophication processes. Our key objectives of the study were to predict long-term algal chlorophyll-a and transparency (water clarity), measured as Secchi depth, in spatially heterogeneous and temporally dynamic reservoirs largely influenced by the Asian monsoon during 2000-2017 and then determine the reservoir trophic state using a multiple linear regression (MLR), support vector machine (SVM) and artificial neural network (ANN). We tested the models to analyze the spatial patterns of the riverine zone (Rz), transitional zone (Tz) and lacustrine zone (Lz) and temporal variations of premonsoon, monsoon and postmonsoon. Monthly physicochemical parameters and precipitation data (2000)(2001)(2002)(2003)(2004)(2005)(2006)(2007)(2008)(2009)(2010)(2011)(2012)(2013)(2014)(2015)(2016)(2017) were used to build up the models of MLR, SVM and ANN and then were confirmed by cross-validation processes. The model of SVM showed better predictive performance than the models of MLR and ANN, in both before validation and after validation. Values of root mean square error (RMSE) and mean absolute error (MAE) were lower in the SVM model, compared to the models of MLR and ANN, indicating that the SVM model has better performance than the MLR and ANN models. The coefficient of determination was higher in the SVM model, compared to the MLR and ANN models. The mean and maximum total suspended solids (TSS), nutrients (total nitrogen (TN) and total phosphorus (TP)), water temperature (WT), conductivity and algal chlorophyll (CHL-a) were in higher concentrations in the riverine zone compared to transitional and lacustrine zone due to surface run-off from the watershed. During the premonsoon and postmonsoon, the average annual rainfall was 59.50 mm and 54.73 mm whereas it was 236.66 mm during the monsoon period. From 2013 to 2017, the trophic state of the reservoir on the basis of CHL-a and SD was from mesotrophic to oligotrophic. Analysis of the importance of input variables indicated that WT, TP, TSS, TN, NP ratios and the rainfall influenced the chlorophyll-a and transparency directly in the reservoir. These findings of the algal chlorophyll-a predictions and Secchi depth may provide key clues for better management strategy in the reservoir.Water 2020, 12, 30 2 of 20 state of the reservoirs and to manage them efficiently, some techniques have to be developed for monitoring and modeling.Mechanistic modeling of the eutrophication is a difficult task due to insufficient observations and the complex behavior of the reservoir ecosystem [5]. One promising action could be the chlorophyll-a and transparency (Secchi depth) prediction by incorporating key environmental variables like as precipitation, water temperature, nutrients, biological oxygen demand and total suspended solids. The reason for using CHL-a and transparency is their wide application as indicators of the eutrophication and turbidit...