Wastewater treatment plants (WWTPs), linking human fecal residues and the environment, are considered as hotspots for the spread of antimicrobial resistance (AMR). In order to evaluate the role of WWTPs and underlying operational parameters for the removal of AMR, the presence and removal efficiency of a selected set of 6 antimicrobial resistance genes (ARGs) and 2 mobile genetic elements (MGEs) was evaluated by means of qPCR in influent and effluent samples from 62 Dutch WWTPs. The role of possible factors impacting the concentrations of ARGs and MGEs in the influent and their removal was identified through statistical analysis. ARGs and the class I integron-integrase gene (intI1) were, on average, removed to a similar extent (1.76 log reduction) or better (+0.30–1.90 logs) than the total bacteria (measured as 16S rRNA gene). In contrast, broad-host-range plasmids (IncP-1) had a significantly increased (p < 0.001) relative abundance after treatment. The presence of healthcare institutions in the area served did only slightly increase the concentrations of ARGs or MGEs in influent. From the extended panel of operational parameters, rainfall, increasing the hydraulic load of the plant, most significantly (p < 0.05) affected the treatment efficiency by decreasing it on average −0.38 logs per time the flow exceeded the average daily flow. Our results suggest that overall, WWTP treatments do not favor the proliferation of the assessed resistance genes but might increase the relative abundance of broad-host-range plasmids of the IncP-1 type.