Seasonal variability in source water can lead to challenges for drinking water providers related to operational optimization and process control in treatment facilities. The objective of this study is to investigate seasonal variability of water quality in municipal small water systems (<3000 residents) supplied by surface waters. Residual chlorine and trihalomethanes (THM) were measured over seven years (2003–2009). Comparisons are made within each system over time, as well as between systems according to the type of their treatment technologies. THM concentrations are generally higher in the summer and autumn. The seasonal variability was generally more pronounced in systems using chlorination plus additional treatment. Chloroform, total THM (TTHM) and residual chlorine concentrations were generally lower in systems using chlorination plus additional treatment. Conversely, brominated THM concentrations were higher in systems using additional treatment. Residual chlorine was highest in the winter and lowest in the spring and summer. Seasonal variations were most pronounced for residual chlorine in systems with additional treatment. There was generally poor correlation between THM concentrations and concentrations of residual chlorine. Further study with these data will be beneficial in finding determinants and indicators for both quantity and variability of disinfection byproducts and other water quality parameters.