Abstract Background Local sustained-release drug delivery systems increase the substantivity of drugs in the oral environment and subsequently enhance their therapeutic effects. This study sought to compare the effects of two commercially available varnishes and one experimental chlorhexidine (CHX) varnish on formation of Streptococcus mutans biofilm. The solubility rates of the varnishes were evaluated as well. Methods Standard acrylic discs were fabricated and divided into groups based on the varnish applied to the disc surfaces, namely, V-varnish, Pascal, and experimental CHX varnish. The effects of the varnishes on S. mutans biofilm were assessed after 48 h. Bacterial growth on the discs was evaluated by colony count and scanning electron microscopy (SEM). Solubility was assessed by immersing the samples in phosphate buffered saline and recording their weight changes at different times. The data were analyzed using one-way ANOVA. Results In the Pascal and experimental varnish groups, the total number of bacteria did not differ from that in the negative control group. The SEM findings confirmed the aforementioned results. Solubility varied significantly among the materials. V-varnish was detached from the surfaces after 2 days. No significant weight change was noted in the experimental varnish group at 14 days, while Pascal varnish showed gradual weight loss from the 5th day to the 10th day and had a plateau thereafter. Conclusions Biofilm formation was inhibited by the Pascal and experimental varnishes but not by the V-varnish. The highest acceptable rate of solubility was observed in the Pascal samples.