Excessive methylmercury (MeHg) accumulation in dietary fish is a global concern due to its harmful effects on human health, however, environmental factors affecting MeHg accumulation in reservoir ecosystems are not clearly known. In this study, we aim to identify the main sources of MeHg in the water column and the critical factors related to MeHg concentration and methylation rate constant (km) in sediment and total Hg concentration in fish using five-year (2016–2020) monitoring data of the five artificial reservoirs. The preliminary mass budgets constructed using the measurement and online data showed that sediment transport dominated over runoff in the long residence time reservoirs (400–475 days), while runoff dominated over sediment transport in the short residence time reservoirs (10 days). Whereas the sediment km showed a comparable variation with the algal biomass, the sediment MeHg concentration and the length-normalized Hg concentration in the barbel steed and bluegill increased in the longer residence time reservoirs with lower algal biomass. As MeHg accumulation in sediment and fish tends to increase in the slowly overturning reservoirs, the hydraulic residence time should be carefully managed to meet the best protection of human health from chronic Hg exposure by fish consumption.