We conducted a large-scale epidemiological investigation to detect the prevalence of Toxoplasma gondii in four marine bivalve shellfish species collected from six representative coastal regions of Weihai, eastern China. Between January 2018 and December 2018, 14,535 marine bivalve shellfish pooled into 2907 samples were randomly collected and examined for T. gondii DNA by a nested PCR assay targeting B1 gene. The results showed that 2.8% (82) of the 2907 pooled samples were tested positive for T. gondii DNA. Two T. gondii genotype (ToxoDB Genotype #9 and ToxoDB Genotype #1) were identified PCR-restriction fragment length polymorphism analysis. Factors that were found significantly associated with the presence of T. gondii DNA in marine bivalve shellfish included the source of samples (being wild) (odds ratio [OR], 3.34; 95% confidence interval [CI], 2.00–5.84; p < 0.01), surface runoff near the sampling site (OR, 2.64; 95% CI, 1.47–4.72; p < 0.01), and presence of cats near the sampling site (OR, 1.77; 95% CI, 1.02–3.07; p = 0.04). Moreover, the prevalence of T. gondii DNA in marine bivalve shellfish correlated with temperature (Pearson’s correlation: R = 0.75, p = 0.0049) and precipitation (R = 0.87, p = 0.00021). These findings provide new insights into the presence of T. gondii DNA in marine bivalve shellfish and highlight the impact of human activity on marine pollution by such an important terrestrial pathogen pollutant.