Both measurement and parameters uncertainties affect a parameter estimation process. To date measurement uncertainties have been considered during water quality parameter estimation in the water distribution systems (WDS). User defined parameter uncertainties have been avoided. It is known that some parameters in the distribution systems can be uncertain. For example, demand affects both the WDS hydraulics and water quality and is one of the most uncertain parameters. This paper considered nodal demand and temporal demand factor as the uncertain parameters when estimating wall decay coefficients of the water quality model. To account uncertainties in demand parameters hydraulic and water quality simulation model, EPANET was run in Monte Carlo Simulation (MCS) with predefined coefficients of variation for the uncertain parameters. Measurement uncertainties were added then with the mean concentration to create observed data. A meta-heuristic search technique, the Shuffled Frog Leaping Algorithm (SFLA) coupled with EPANET was used then to calibrate the wall decay parameters. Results show that parameters uncertainties can be as important as measurement uncertainties. Measurement uncertainty does not compensate parameters' uncertainties rather it increases the prediction errors.