Calibration and uncertainty analysis of a complex, over-parameterized environmental model such as the Soil and Water Assessment Tool (SWAT) requires thousands of simulation runs and multiple calibration iterations. A parallel calibration system is thus desired that can be deployed on cloud-based architectures for reducing calibration runtime. This paper presents a cloud-based calibration and uncertainty analysis system called LCC-SWAT that is designed for SWAT models. Two optimization techniques, sequential uncertainty fitting (SUFI-2) and dynamically dimensioned search (DDS), have been implemented in LCC-SWAT. Moreover, the cloud-based system has been deployed on the Southern Ontario Smart Computing Innovation Platform's (SOSCIP) Cloud Analytics platform for diagnostic assessment of parallel calibration runtime on both single-node and multi-node CPU architectures. Unlike other calibrations/uncertainty analysis systems developed on the cloud, this system is capable of generating a comprehensive set of statistical information automatically, which facilitates broader analyses of the performance of the SWAT models. Experimental results on SWAT models of different complexities showed that LCC-SWAT can reduce runtime significantly. The runtime reduction is more pronounced for more complex and computationally intensive models. However, the reported runtime efficiency is significantly higher for single node systems. Comparative experiments with DDS and SUFI-2 show that parallel DDS outperforms parallel SUFI-2 in terms of both parameter identifiability and reducing uncertainty in model simulations. LCC-SWAT is a flexible calibration system and other optimization algorithms and asynchronous parallelization strategies can be added to it in future.