Methylmercury concentrations [MeHg] in whole water were measured in 28 prairie wetland ponds in central Saskatchewan between 2006 and 2012. Ponds fell into four land use categories (established grass, recent grass, traditional cultivated, and certified organic cultivated) and two water level patterns (“Mainly Wet” ponds stayed wet at least until October and “Mainly Dry” ponds dried up each summer). Despite similar atmospheric Hg deposition, average [MeHg] and proportion of total Hg that was MeHg (%MeHg) were higher in water from ponds surrounded with established grass or organic farming; this trend may be driven by high [MeHg] at one Organic site. A stronger relationship was observed with water level patterns. Average [MeHg] and %MeHg were significantly higher in Mainly Wet ponds compared to Mainly Dry ponds. Higher [MeHg] in Mainly Wet ponds were correlated with much higher dissolved organic carbon (DOC) and sulfate (SO4−2) concentrations and higher specific UV absorbance of DOC. We suggest that prairie wetland ponds may not fit the accepted paradigm that wetlands with high [SO4−2] show inhibition of Hg methylation. Our work suggests controls such as the chemical nature of DOC or redox fluctuations in hydrologically dynamic systems may be important in determining net [MeHg] in these sites.