<p>The National Environmental Specimen Bank of the Ministry of Environment of the Republic of Korea has selected the common carp as a target species for monitoring freshwater environmental pollutants. This study analyzed total mercury (THg) concentrations in the muscle of a carp collected from the Han River and Yeongsan River during 2012–2021 to evaluate regional and periodic trends. Two-way analysis of covariance and the generalized linear model were applied to correct differences in mercury concentration depending on the carp length. The analysis results revealed that carp length had a significant impact on mercury concentrations, which tended to increase with length. The regional and periodic interaction effect was also found to vary, indicating different periodic change patterns of mercury concentrations for both rivers. The Han River exhibited significant periodic mercury concentrations, contrary to the Yeongsan River. Post-hoc analysis results revealed a significant reduction between periods A and C in the Han River, reflecting the effects of implemented environmental regulatory policies and changing industrial activities in the basin. THg concentrations in the carp from both rivers did not exceed local and international food standards concentrations; however, several samples exceeded the reproduction concentration threshold, indicating an ecological risk assessment requirement. This study quantitatively assessed the effects of environmental regulations and regional differences using long-term mercury concentration monitoring results from the two regions. As common carp are occasionally consumed as a food resource in East Asia, including Korea, these findings have implications for both ecological risks and potential human health risk assessments.</p>